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BACKGROUND: Patients with relapsed or refractory mantle-cell lymphoma who have disease progression during or after the receipt of Bruton's tyrosine kinase (BTK) inhibitor therapy have a poor prognosis. KTE-X19, an anti-CD19 chimeric antigen receptor (CAR) T-cell therapy, may have benefit in patients with relapsed or refractory mantle-cell lymphoma. METHODS: In a multicenter, phase 2 trial, we evaluated KTE-X19 in patients with relapsed or refractory mantle-cell lymphoma. Patients had disease that had relapsed or was refractory after the receipt of up to five previous therapies; all patients had to have received BTK inhibitor therapy previously. Patients underwent leukapheresis and optional bridging therapy, followed by conditioning chemotherapy and a single infusion of KTE-X19 at a dose of 2×106 CAR T cells per kilogram of body weight. The primary end point was the percentage of patients with an objective response (complete or partial response) as assessed by an independent radiologic review committee according to the Lugano classification. Per the protocol, the primary efficacy analysis was to be conducted after 60 patients had been treated and followed for 7 months. RESULTS: A total of 74 patients were enrolled. KTE-X19 was manufactured for 71 patients and administered to 68. The primary efficacy analysis showed that 93% (95% confidence interval [CI], 84 to 98) of the 60 patients in the primary efficacy analysis had an objective response; 67% (95% CI, 53 to 78) had a complete response. In an intention-to-treat analysis involving all 74 patients, 85% had an objective response; 59% had a complete response. At a median follow-up of 12.3 months (range, 7.0 to 32.3), 57% of the 60 patients in the primary efficacy analysis were in remission. At 12 months, the estimated progression-free survival and overall survival were 61% and 83%, respectively. Common adverse events of grade 3 or higher were cytopenias (in 94% of the patients) and infections (in 32%). Grade 3 or higher cytokine release syndrome and neurologic events occurred in 15% and 31% of patients, respectively; none were fatal. Two grade 5 infectious adverse events occurred. CONCLUSIONS: KTE-X19 induced durable remissions in a majority of patients with relapsed or refractory mantle-cell lymphoma. The therapy led to serious and life-threatening toxic effects that were consistent with those reported with other CAR T-cell therapies. (Funded by Kite, a Gilead company; ZUMA-2 ClinicalTrials.gov number, NCT02601313.).
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Antígenos CD19/uso terapêutico , Imunoterapia Adotiva , Linfoma de Célula do Manto/terapia , Receptores de Antígenos Quiméricos/antagonistas & inibidores , Adulto , Idoso , Antineoplásicos/uso terapêutico , Terapia Combinada , Humanos , Imunoterapia Adotiva/efeitos adversos , Infusões Intravenosas , Leucaférese , Linfoma de Célula do Manto/tratamento farmacológico , Linfoma de Célula do Manto/mortalidade , Pessoa de Meia-Idade , Recidiva , Análise de Sobrevida , Linfócitos T/transplante , Vidarabina/análogos & derivados , Vidarabina/uso terapêuticoRESUMO
AIMS: Acalabrutinib, a selective Bruton tyrosine kinase inhibitor, is approved for the treatment of mantle cell lymphoma and chronic lymphocytic leukaemia. Many critically ill patients are unable to swallow and need oral medications to be delivered via a nasogastric (NG) tube. Furthermore, critically ill patients are typically administered proton-pump inhibitors (PPIs) to prevent stress ulcers. Concomitant administration with PPIs reduces acalabrutinib exposure and is not currently recommended. To evaluate acalabrutinib in subjects co-administered with PPIs who require NG delivery, a phase 1, open-label, randomized, crossover, single-dose study was conducted in healthy subjects. METHODS: The study assessed the relative bioavailability of an acalabrutinib suspension-in regular, degassed Coca-Cola-administered via NG tube (Acala-NG) versus the pharmacokinetics (PK) of an acalabrutinib capsule administered orally with water. In addition, the PPI effect was evaluated by comparing the PK following Acala-NG in the presence or absence of rabeprazole. RESULTS: Exposure of acalabrutinib and its active metabolite (ACP-5862) were comparable following administration of Acala-NG versus the oral capsule (Geo mean ratio, % ref [90% confidence interval, CI]: acalabrutinib AUCinf : 103 [93-113]; Cmax : 144 [120-173]). In addition, exposure was similar following administration of Acala-NG with and without a PPI (Geo mean ratio, % ref [90% CI]: acalabrutinib AUCinf : 105 [79-138]; Cmax : 95 [66-137]). No safety or tolerability concerns were observed, and all adverse events were mild and resolved without treatment. CONCLUSIONS: Acala-NG with or without a PPI is safe and well-tolerated without impeding bioavailability.
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Estado Terminal , Inibidores da Bomba de Prótons , Adulto , Benzamidas , Disponibilidade Biológica , Estudos Cross-Over , Voluntários Saudáveis , Humanos , Inibidores da Bomba de Prótons/efeitos adversos , Inibidores da Bomba de Prótons/farmacocinética , Pirazinas , SuspensõesRESUMO
Automotive millimeter-wave (MMW) radar is essential in autonomous vehicles due to its robustness in all weather conditions. Traditional commercial automotive radars are limited by their resolution, which makes the object classification task difficult. Thus, the concept of a new generation of four-dimensional (4D) imaging radar was proposed. It has high azimuth and elevation resolution and contains Doppler information to produce a high-quality point cloud. In this paper, we propose an object classification network named Radar Transformer. The algorithm takes the attention mechanism as the core and adopts the combination of vector attention and scalar attention to make full use of the spatial information, Doppler information, and reflection intensity information of the radar point cloud to realize the deep fusion of local attention features and global attention features. We generated an imaging radar classification dataset and completed manual annotation. The experimental results show that our proposed method achieved an overall classification accuracy of 94.9%, which is more suitable for processing radar point clouds than the popular deep learning frameworks and shows promising performance.
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Hand gesture recognition technology plays an important role in human-computer interaction and in-vehicle entertainment. Under in-vehicle conditions, it is a great challenge to design gesture recognition systems due to variable driving conditions, complex backgrounds, and diversified gestures. In this paper, we propose a gesture recognition system based on frequency-modulated continuous-wave (FMCW) radar and transformer for an in-vehicle environment. Firstly, the original range-Doppler maps (RDMs), range-azimuth maps (RAMs), and range-elevation maps (REMs) of the time sequence of each gesture are obtained by radar signal processing. Then we preprocess the obtained data frames by region of interest (ROI) extraction, vibration removal algorithm, background removal algorithm, and standardization. We propose a transformer-based radar gesture recognition network named RGTNet. It fully extracts and fuses the spatial-temporal information of radar feature maps to complete the classification of various gestures. The experimental results show that our method can better complete the eight gesture classification tasks in the in-vehicle environment. The recognition accuracy is 97.56%.
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Gestos , Radar , Algoritmos , Humanos , Reconhecimento Automatizado de Padrão , Processamento de Sinais Assistido por ComputadorRESUMO
A zeolite-like gyroidal MOF (denoted as SCNU-1) constructed with Cu ions and 4-(1H-imidazo[4,5-f][1,10]phenanthrolin-2-yl)phenol has a featured interpenetrating uninodal utc-c network which is for the first time found in the real structure. Moreover, SCNU-1 exhibits high thermal (>773 K), solvent, and acid/base stabilities; the largest CO2 affinity, 90 kJ/mol, among the MOFs functionalized with an aromatic hydroxyl group; and excellent CO2/N2 selectivity.
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Antígenos CD19/uso terapêutico , Linfoma Difuso de Grandes Células B/terapia , Recidiva Local de Neoplasia/terapia , Adulto , Idoso , Produtos Biológicos , Feminino , Seguimentos , Humanos , Imunoterapia Adotiva , Linfoma Difuso de Grandes Células B/imunologia , Linfoma Difuso de Grandes Células B/patologia , Masculino , Pessoa de Meia-Idade , Recidiva Local de Neoplasia/imunologia , Recidiva Local de Neoplasia/patologia , Prognóstico , Taxa de Sobrevida , Adulto JovemRESUMO
The genetic architecture of many phenotypic traits is such that genes often contribute to multiple traits, and mutations in these genes can therefore affect multiple phenotypes. These pleiotropic interactions often manifest as tradeoffs between traits where improvement in one property entails a cost in another. The life cycles of many pathogens include periods of growth within a host punctuated with transmission events, such as passage through a digestive tract or a passive stage of exposure in the environment. Populations exposed to such fluctuating selective pressures are expected to acquire mutations showing tradeoffs between reproduction within and survival outside of a host. We selected for individual mutations under fluctuating selective pressures for a ssDNA microvirid bacteriophage by alternating selection for increased growth rate with selection on biophysical properties of the phage capsid in high-temperature or low-pH conditions. Surprisingly, none of the seven unique mutations identified showed a pleiotropic cost; they all improved both growth rate and pH or temperature stability, suggesting that single mutations even in a simple genetic system can simultaneously improve two distinct traits. Selection on growth rate alone revealed tradeoffs, but some mutations still benefited both traits. Tradeoffs were therefore prevalent when selection acted on a single trait, but payoffs resulted when multiple traits were selected for simultaneously. We employed a molecular-dynamics simulation method to determine the mechanisms underlying beneficial effects for three heat-shock mutations. All three mutations significantly enhanced the affinities of protein-protein interfacial bindings, thereby improving capsid stability. The ancestral residues at the mutation sites did not contribute to protein-protein interfacial binding, indicating that these sites acquired a new function. Computational models, such as those used here, may be used in future work not only as predictive tools for mutational effects on protein stability but, ultimately, for evolution.
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Adaptação Fisiológica/genética , Microvirus/fisiologia , Seleção Genética , Capsídeo/metabolismo , Aptidão Genética , Resposta ao Choque Térmico/genética , Concentração de Íons de Hidrogênio , Microvirus/química , Microvirus/genética , Microvirus/crescimento & desenvolvimento , Mutação , Temperatura , Proteínas Virais/genética , Proteínas Virais/metabolismoRESUMO
Hydrogen sulfide (H2 S), a commonly known toxic gas compound, possesses unique chemical features that allow this small solute molecule to quickly diffuse through cell membranes. Taking advantage of the recent orthogonal space tempering (OST) method, we comparatively mapped the transmembrane free energy landscapes of H2 S and its structural analogue, water (H2 O), seeking to decipher the molecular determinants that govern their drastically different permeabilities. As revealed by our OST sampling results, in contrast to the highly polar water solute, hydrogen sulfide is evidently amphipathic, and thus inside membrane is favorably localized at the interfacial region, that is, the interface between the polar head-group and nonpolar acyl chain regions. Because the membrane binding affinity of H2 S is mainly governed by its small hydrophobic moiety and the barrier height inbetween the interfacial region and the membrane center is largely determined by its moderate polarity, the transmembrane free energy barriers to encounter by this toxic molecule are very small. Moreover when H2 S diffuses from the bulk solution to the membrane center, the above two effects nearly cancel each other, so as to lead to a negligible free energy difference. This study not only explains why H2 S can quickly pass through cell membranes but also provides a practical illustration on how to use the OST free energy sampling method to conveniently analyze complex molecular processes. © 2015 Wiley Periodicals, Inc.
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Membrana Celular/metabolismo , Sulfeto de Hidrogênio/metabolismo , Água/metabolismo , Membrana Celular/química , Permeabilidade da Membrana Celular , Simulação por Computador , Difusão , Humanos , Sulfeto de Hidrogênio/química , Interações Hidrofóbicas e Hidrofílicas , Modelos Biológicos , Termodinâmica , Água/químicaRESUMO
A direct-infusion electrospray ionization triple-quadrupole mass spectrometry method with multiple reaction monitoring (MRM) was employed to measure 264 lipid analytes extracted from leaves of Arabidopsis thaliana subjected to mechanical wounding. The method provided precise measurements with an average coefficient of variation of 6.1%. Lipid classes analyzed comprised galactolipids and phospholipids (including monoacyl molecular species, molecular species with oxidized acyl chains, phosphatidic acids (PAs)), tri- and tetra-galactosyldiacylglycerols (TrGDGs and TeGDGs), head-group-acylated galactolipids, and head-group-acylated phosphatidylglycerol (acPG), sulfoquinovosyldiacylglycerols (SQDGs), sphingolipids, di- and tri-acylglycerols (DAGs and TAGs), and sterol derivatives. Of the 264 lipid analytes, 254 changed significantly in response to wounding. In general, levels of structural lipids decreased, whereas monoacyl molecular species, galactolipids and phosphatidylglycerols (PGs) with oxidized fatty acyl chains, PAs, TrGDGs, TeGDGs, TAGs, head-group-acylated galactolipids, acPG, and some sterol derivatives increased, many transiently. The observed changes are consistent with activation of lipid oxidizing, hydrolyzing, glycosylating, and acylating activities in the wounding response. Correlation analysis of the levels of lipid analytes across individual control and treated plants was used to construct a lipid dendrogram and to define clusters and sub-clusters of lipid analytes, each composed of a group of lipids which occurred in a coordinated manner. Current knowledge of metabolism supports the notion that observed sub-clusters comprise lipids generated by a common enzyme and/or metabolically downstream of a common enzyme. This work demonstrates that co-occurrence analysis, based on correlation of lipid levels among plants, is a powerful approach to defining lipids generated in vivo by a common enzymatic pathway.
Assuntos
Arabidopsis/metabolismo , Lipídeos/análise , Lipídeos/química , Folhas de Planta/metabolismo , Galactolipídeos/análise , Galactolipídeos/metabolismo , Ácidos Fosfatídicos/análise , Ácidos Fosfatídicos/metabolismo , Fosfolipídeos/análise , Folhas de Planta/química , Espectrometria de Massas por Ionização por Electrospray/métodosRESUMO
Modification of transparent metal oxide (MOx) surfaces with organic monolayers is widely employed to tailor the properties of interfaces in organic electronic devices, and MOx substrates modified with light-absorbing chromophores are a key component of dye-sensitized solar cells (DSSCs). The effects of an organic modifier on the performance of a MOx-based device are frequently assessed by performing experiments on model monolayer|MOx interfaces, where an "inert" MOx (e.g., Al2O3) is used as a control for an "active" MOx (e.g., TiO2). An underlying assumption in these studies is that the structure of the MOx-monolayer complex is similar between different metal oxides. The validity of this assumption was examined in the present study. Using UV-Vis attenuated total reflection spectroscopy, we measured the mean dipole tilt angle of 4,4'-(anthracene-9,10-diyl)bis(4,1-phenylene)diphosphonic acid (A1P) adsorbed on indium tin oxide (ITO), TiO2, ZrO2, and Al2O3. When the surface roughness of the MOx substrate and the surface coverage (ð¤) of the A1P film were constant, the molecular orientation of A1P was the same on these substrates. The study was extended to 4,4'-(anthracene-9,10-diyl)bis(4,1-phenylene)dicarboxylic acid (A1C) adsorbed on the same group of MOx substrates. The mean tilt angle of A1C and A1P films on ITO was the same, which is likely due the intermolecular interactions resulting from the high and approximately equal ð¤ of both films. Comparing A1C films at the same ð¤ on TiO2 and Al2O3 having the same surface roughness, there was no difference in the mean tilt angle. MD simulations of A1C and A1P on TiO2 produced nearly identical tilt angle distributions, which supports the experimental findings. This study provides first experimental support for the assumption that the structure of the MOx-modifer film is the same on an "active" substrate vs. a "inert" control substrate.
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Molecular dynamics sampling can be enhanced via the promoting of potential energy fluctuations, for instance, based on a Hamiltonian modified with the addition of a potential-energy-dependent biasing term. To overcome the diffusion sampling issue, which reveals the fact that enlargement of event-irrelevant energy fluctuations may abolish sampling efficiency, the essential energy space random walk (EESRW) approach was proposed earlier. To more effectively accelerate the sampling of solute conformations in aqueous environment, in the current work, we generalized the EESRW method to a two-dimension-EESRW (2D-EESRW) strategy. Specifically, the essential internal energy component of a focused region and the essential interaction energy component between the focused region and the environmental region are employed to define the two-dimensional essential energy space. This proposal is motivated by the general observation that in different conformational events, the two essential energy components have distinctive interplays. Model studies on the alanine dipeptide and the aspartate-arginine peptide demonstrate sampling improvement over the original one-dimension-EESRW strategy; with the same biasing level, the present generalization allows more effective acceleration of the sampling of conformational transitions in aqueous solution. The 2D-EESRW generalization is readily extended to higher dimension schemes and employed in more advanced enhanced-sampling schemes, such as the recent orthogonal space random walk method.
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Alanina/química , Ácido Aspártico/química , Dipeptídeos/química , Simulação de Dinâmica Molecular , Água/química , Modelos Moleculares , Conformação Molecular , SoluçõesRESUMO
Acalabrutinib is a Bruton tyrosine kinase (BTK) inhibitor approved to treat adults with chronic lymphocytic leukemia, small lymphocytic lymphoma, or previously treated mantle cell lymphoma. As the bioavailability of the acalabrutinib capsule (AC) depends on gastric pH for solubility and is impaired by acid-suppressing therapies, coadministration with proton-pump inhibitors (PPIs) is not recommended. Three studies in healthy subjects (N = 30, N = 66, N = 20) evaluated the pharmacokinetics (PKs), pharmacodynamics (PDs), safety, and tolerability of acalabrutinib maleate tablet (AT) formulated with pH-independent release. Subjects were administered AT or AC (orally, fasted state), AT in a fed state, or AT in the presence of a PPI, and AT or AC via nasogastric (NG) route. Acalabrutinib exposures (geometric mean [% coefficient of variation, CV]) were comparable for AT versus AC (AUCinf 567.8 ng h/mL [36.9] vs 572.2 ng h/mL [38.2], Cmax 537.2 ng/mL [42.6] vs 535.7 ng/mL [58.4], respectively); similar results were observed for acalabrutinib's active metabolite (ACP-5862) and for AT-NG versus AC-NG. The geometric mean Cmax for acalabrutinib was lower when AT was administered in the fed versus the fasted state (Cmax 255.6 ng/mL [%CV, 46.5] vs 504.9 ng/mL [49.9]); AUCs were similar. For AT + PPI, geometric mean Cmax was lower (371.9 ng/mL [%CV, 81.4] vs 504.9 ng/mL [49.9]) and AUCinf was higher (AUCinf 694.1 ng h/mL [39.7] vs 559.5 ng h/mL [34.6]) than AT alone. AT and AC were similar in BTK occupancy. Most adverse events were mild with no new safety concerns. Acalabrutinib formulations were comparable and AT could be coadministered with PPIs, food, or via NG tube without affecting the PKs or PDs.
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Inibidores da Bomba de Prótons , Pirazinas , Adulto , Humanos , Disponibilidade Biológica , Equivalência Terapêutica , Inibidores da Bomba de Prótons/efeitos adversos , Inibidores da Bomba de Prótons/farmacocinética , Pirazinas/efeitos adversos , Pirazinas/farmacocinética , Comprimidos , Inibidores de Proteínas Quinases/efeitos adversos , Inibidores de Proteínas Quinases/farmacocinéticaRESUMO
Allosteric activators are generally believed to shift the equilibrium distribution of enzyme conformations to favor a catalytically productive structure; the kinetics of conformational exchange is seldom addressed. Several observations suggested that the usual allosteric mechanism might not apply to the activation of IMP dehydrogenase (IMPDH) by monovalent cations. Therefore, we investigated the mechanism of K(+) activation in IMPDH by delineating the kinetic mechanism in the absence of monovalent cations. Surprisingly, the K(+) dependence of k(cat) derives from the rate of flap closure, which increases by ≥65-fold in the presence of K(+). We performed both alchemical free energy simulations and potential of mean force calculations using the orthogonal space random walk strategy to computationally analyze how K(+) accelerates this conformational change. The simulations recapitulate the preference of IMPDH for K(+), validating the computational models. When K(+) is replaced with a dummy ion, the residues of the K(+) binding site relax into ordered secondary structure, creating a barrier to conformational exchange. K(+) mobilizes these residues by providing alternate interactions for the main chain carbonyls. Potential of mean force calculations indicate that K(+) changes the shape of the energy well, shrinking the reaction coordinate by shifting the closed conformation toward the open state. This work suggests that allosteric regulation can be under kinetic as well as thermodynamic control.
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Regulação Alostérica/efeitos dos fármacos , IMP Desidrogenase/química , Potássio/farmacologia , Simulação por Computador , Cryptosporidium parvum/enzimologia , Ativação Enzimática , IMP Desidrogenase/efeitos dos fármacos , IMP Desidrogenase/metabolismo , Cinética , Simulação de Dinâmica Molecular , Conformação Proteica/efeitos dos fármacosRESUMO
In the past few decades, many ingenious efforts have been made in the development of free-energy simulation methods. Because complex systems often undergo nontrivial structural transition during state switching, achieving efficient free-energy calculation can be challenging. As identified earlier, the "Hamiltonian" lagging, which reveals the fact that necessary structural relaxation falls behind the order parameter move, has been a primary problem for generally low free-energy simulation efficiency. Here, we propose an algorithm by achieving a random walk in both the order parameter space and its generalized force space; thereby, the order parameter move and the required conformational relaxation can be efficiently synchronized. As demonstrated in both the alchemical transition and the conformational transition, a leapfrog improvement in free-energy simulation efficiency can be obtained; for instance, (i) it allows us to solve a notoriously challenging problem: accurately predicting the pK(a) value of a buried titratable residue, Asp-66, in the interior of the V66E staphylococcal nuclease mutant, and (ii) it allows us to gain superior efficiency over the metadynamics algorithm.
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Simulação por Computador , Modelos Químicos , Termodinâmica , Difusão , Concentração de Íons de Hidrogênio , Métodos , Nuclease do Micrococo/química , Nuclease do Micrococo/genética , Conformação ProteicaRESUMO
Cerebral edema following chimeric antigen receptor (CAR) T-cell therapy can be fatal. ZUMA-2 is a pivotal phase 2, multicenter study evaluating KTE-X19, an autologous anti-CD19 CAR T-cell therapy, in relapsed/refractory mantle cell lymphoma. We describe a 65-year-old patient in ZUMA-2 who developed cerebral edema following CAR T-cell therapy and had complete recovery after multimodality clinical intervention including rabbit antithymocyte globulin (ATG). Biomarker results show early and robust CAR T-cell expansion and related induction of inflammatory cytokines, followed by rapid declines in CAR T-cell and proinflammatory cytokine levels after ATG administration. This clinical profile highlights a potential relevance of ATG in treating severe CAR T-cell-related neurotoxicity.
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Terapia Baseada em Transplante de Células e Tecidos/efeitos adversos , Linfoma de Célula do Manto/complicações , Linfoma de Célula do Manto/tratamento farmacológico , Receptores de Antígenos Quiméricos/uso terapêutico , Idoso , Humanos , MasculinoRESUMO
Metal ion linked multilayers is a unique motif to spatially control and geometrically restrict molecules on a metal oxide surface and is of interest in a number of promising applications. Here we use a bilayer composed of a metal oxide surface, an anthracene annihilator molecule, Zn(II) linking ion, and porphyrin sensitizers to probe the influence of the position of the metal ion binding site on energy transfer, photon upconversion, and photocurrent generation. Despite being energetically similar, varying the position of the carboxy metal ion binding group (i.e. ortho, meta, para) of the Pt(II) tetraphenyl porphyrin sensitizer had a large impact on energy transfer rates and upconverted photocurrent that can be attributed to differences in their geometries. From polarized attenuated total reflectance measurements of the bilayers on ITO, we found that the orientation of the first layer (anthracene) was largely unperturbed by subsequent layers. However, the tilt angle of the porphyrin plane varies dramatically from 41° to 64° to 57° for the para-, meta-, and ortho-COOH substituted porphyrin molecules, which is likely responsible for the variation in energy transfer rates. We go on to show using molecular dynamics simulations that there is considerable flexibility in porphyrin orientation, indicating that an average structure is insufficient to predict the ensemble behavior. Instead, even a small subset of the population with highly favorable energy transfer rates can be the primary driver in increasing the likelihood of energy transfer. Gaining control of the orientation and its distribution will be a critical step in maximizing the potential of the metal ion linked structures.
RESUMO
To overcome the pseudoergodicity problem, conformational sampling can be accelerated via generalized ensemble methods, e.g., through the realization of random walks along prechosen collective variables, such as spatial order parameters, energy scaling parameters, or even system temperatures or pressures, etc. As usually observed, in generalized ensemble simulations, hidden barriers are likely to exist in the space perpendicular to the collective variable direction and these residual free energy barriers could greatly abolish the sampling efficiency. This sampling issue is particularly severe when the collective variable is defined in a low-dimension subset of the target system; then the "Hamiltonian lagging" problem, which reveals the fact that necessary structural relaxation falls behind the move of the collective variable, may be likely to occur. To overcome this problem in equilibrium conformational sampling, we adopted the orthogonal space random walk (OSRW) strategy, which was originally developed in the context of free energy simulation [L. Zheng, M. Chen, and W. Yang, Proc. Natl. Acad. Sci. U.S.A. 105, 20227 (2008)]. Thereby, generalized ensemble simulations can simultaneously escape both the explicit barriers along the collective variable direction and the hidden barriers that are strongly coupled with the collective variable move. As demonstrated in our model studies, the present OSRW based generalized ensemble treatments show improved sampling capability over the corresponding classical generalized ensemble treatments.
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Alanina/química , Simulação por Computador , Dipeptídeos/química , Modelos Químicos , Termodinâmica , Pressão , Conformação Proteica , Estrutura Secundária de Proteína , TemperaturaRESUMO
We conduct classical molecular dynamics simulations to investigate isobaric melting of defective Cu solids with only one type of defect: intrinsic or extrinsic stacking faults. We characterize bulk melting and nucleation of melt in terms of order parameters, liquid cluster analysis, and the mean-first-passage-time method. The stacking faults induce negligible reduction in the temperature at melting, and the amount of superheating in these defective solids is the same as the perfect solids. Both homogeneous and heterogeneous nucleations of melt are observed. The existence of the stacking faults only slightly increases the nucleation rate and the probability of nucleation at heterogeneous nucleation sites. Such observations can be attributed to the low energy of the stacking faults and the extremely high heating rates in molecular dynamics simulations. These results underscore the necessity of considering the effects of rate and defect when interpreting experimental and simulation results as regards, e.g., phase boundaries.
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Cobre/química , Teoria Quântica , CongelamentoRESUMO
Recently, accelerated molecular dynamics (AMD) technique was generalized to realize essential energy space random walks so that further sampling enhancement and effective localized enhanced sampling could be achieved. This method is especially meaningful when essential coordinates of the target events are not priori known; moreover, the energy space metadynamics method was also introduced so that biasing free energy functions can be robustly generated. Despite the promising features of this method, due to the nonequilibrium nature of the metadynamics recursion, it is challenging to rigorously use the data obtained at the recursion stage to perform equilibrium analysis, such as free energy surface mapping; therefore, a large amount of data ought to be wasted. To resolve such problem so as to further improve simulation convergence, as promised in our original paper, we are reporting an alternate approach: the adaptive-length self-healing (ALSH) strategy for AMD simulations; this development is based on a recent self-healing umbrella sampling method. Here, the unit simulation length for each self-healing recursion is increasingly updated based on the Wang-Landau flattening judgment. When the unit simulation length for each update is long enough, all the following unit simulations naturally run into the equilibrium regime. Thereafter, these unit simulations can serve for the dual purposes of recursion and equilibrium analysis. As demonstrated in our model studies, by applying ALSH, both fast recursion and short nonequilibrium data waste can be compromised. As a result, combining all the data obtained from all the unit simulations that are in the equilibrium regime via the weighted histogram analysis method, efficient convergence can be robustly ensured, especially for the purpose of free energy surface mapping.
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Simulação por Computador , Termodinâmica , Estudos de Viabilidade , Propriedades de Superfície , Fatores de TempoRESUMO
Recently, we developed a generalized ensemble based free energy simulation technique, the simulated scaling (SS) method [Li et al., J. Chem. Phys. 126, 024106 (2007)]. In the SS simulations, random walks in the scaling parameter space are realized and free energy values can be conveniently estimated based on trial biasing weights. To improve free energy convergence in the SS simulations, we adopt a recent adaptive algorithm to systematically optimize the scaling parameter intervals; here, the optimization target is the round-trip rate between two end chemical states. As demonstrated in our model studies on the solvation of chloride ion and methane, free energy convergence can be greatly improved when the round-trip rates are accelerated.