Petaloid bimetallic metal-organic frameworks derived ZnCo2O4/ZnO nanosheets enabled intermittent lithiophilic model for dendrite-free lithium metal anode.

The application of lithium metal anode (LMA) is hindered by its poor cycle life which could be caused by lithium dendrite and critical volume change during cycling. Our group previously proposed an intermittent lithiophilic model for three-dimensional (3D) composite LMA, however, the lithium electrodeposition behavior was not discussed. To verify this model, this work proposed a facile design of a petaloid bimetallic metal-organic frameworks (MOFs) derived ZnCo2O4/ZnO (ZZCO) nanosheets modified carbon cloth (CC), i.e. CC@ZZCO, as a 3D host to achieve the intermittent deposition of lithium (Li). The material characterizations, density functional theory (DFT) calculations, lithium electrodeposition behaviors, and the electrochemical tests were investigated and the intermittent lithium deposition behavior was firstly confirmed. Thanks to the intermittent lithiophilic model, the composite LMA enabled a prolonged lifespan of 1500 h in a symmetrical cell under challenging conditions of 5 mA h cm-2 and 5 mA cm-2, and can maintain stable at 10C with an ultrahigh specific capacity of 110 mAh/g. Furthermore, it can also be coupled with a LiNi0.5Co0.2Mn0.3O2 (NCM523) and a high surface load of LiFePO4 (LFP) cathode (11.5 mg cm-2). This research might open a window for the understanding of the Li deposition behavior and pave the way to develop other alkali-metal-ion batteries.

Sequence-Dependent Orientational Coupling and Electrostatic Attraction in Cation-Mediated DNA-DNA Interactions.

Condensation of DNA is vital for its biological functions and controlled nucleic acid assemblies. However, the mechanisms of DNA condensation are not fully understood due to the inability of experiments to access cation distributions and the complex interplay of energetic and entropic forces during assembly. By constructing free energy surfaces using exhaustive sampling and detailed analysis of cation distributions, we elucidate the mechanism of DNA condensation in different salt conditions and with different DNA sequences. We found that DNA condensation is facilitated by the correlated dynamics of the localized cations at the grooves of DNA helices. These dynamics are strongly dependent on the salt conditions and DNA sequences. In the presence of magnesium ions, major groove binding facilitates attraction. In contrast, in the presence of polyvalent cations, minor groove binding serves to create charge patterns, leading to condensation. Our findings present a novel advancement in the field and have broad implications for understanding and controlling nucleic acid complexes in vivo and in vitro.

Study of Predominant Dynamics on the O3-Type Layered Transition-Metal Oxide Cathode by Electrochemical Impedance Spectroscopy for Sodium-Ion Batteries.

The layered transition metal oxides (NaxTMO2) are the most attractive cathode options for the rechargeable sodium-ion batteries (SIBs) owing to their high specific capacity, outstanding sodium desorption ability, and high average operating voltage. However, the kinetic behaviors corresponding to complex and prominent phase transitions are still perplexing. Here, we investigate the detailed electrochemical kinetic characteristics of the NaNi1/3Fe1/3Mn1/3O2 electrode by electrochemical impedance spectroscopy (EIS) in three-electrode configurations assistance with the distribution of relaxation times (DRT) and trusted equivalent circuit models numerical analysis. The complex and prominent phase transformations evolution of O3-P3-O3' in the charge process and O3'-P3'-O3 during the discharge process are reflected at different degrees of frequencies and potentials, and significant contributions for the charge transfer step are established on this basis. As the charge and discharge proceed, the influence on charge transfer process by phase transform will be weak, however, which still has some expression and can be caught by EIS assistance with DRT. Additionally, a diagrammatic model for Na+ extraction/insertion is established to illustrate the physicochemical reaction mechanism in the NaNi1/3Fe1/3Mn1/3O2 electrode. The results definitely provide certain scientific thoughts and guiding principles for the commercialization of NaxTMO2 in SIBs.

Sequence similarity governs generalizability of de novo deep learning models for RNA secondary structure prediction.

Making no use of physical laws or co-evolutionary information, de novo deep learning (DL) models for RNA secondary structure prediction have achieved far superior performances than traditional algorithms. However, their statistical underpinning raises the crucial question of generalizability. We present a quantitative study of the performance and generalizability of a series of de novo DL models, with a minimal two-module architecture and no post-processing, under varied similarities between seen and unseen sequences. Our models demonstrate excellent expressive capacities and outperform existing methods on common benchmark datasets. However, model generalizability, i.e., the performance gap between the seen and unseen sets, degrades rapidly as the sequence similarity decreases. The same trends are observed from several recent DL and machine learning models. And an inverse correlation between performance and generalizability is revealed collectively across all learning-based models with wide-ranging architectures and sizes. We further quantitate how generalizability depends on sequence and structure identity scores via pairwise alignment, providing unique quantitative insights into the limitations of statistical learning. Generalizability thus poses a major hurdle for deploying de novo DL models in practice and various pathways for future advances are discussed.

Ion Transport and Electrochemical Reaction in LiNi0.5Co0.2Mn0.3O2-Based High Energy/Power Lithium-Ion Batteries.

The high energy/power lithium-ion battery using LiNi0.5Co0.2Mn0.3O2 (NCM523 HEP LIB) has an excellent trade-off between specific capacity, cost, and stable thermal characteristics. However, it still brings a massive challenge for power improvement under low temperatures. Deeply understanding the electrode interface reaction mechanism is crucial to solving this problem. This work studies the impedance spectrum characteristics of commercial symmetric batteries under different states of charge (SOCs) and temperatures. The changing tendencies of the Li+ diffusion resistance Rion and charge transfer resistance Rct with temperature and SOC are explored. Moreover, one quantitative parameter, § ≡ Rct/Rion, is introduced to identify the boundary conditions of the rate control step inside the porous electrode. This work points out the direction to design and improve performance for commercial HEP LIB with common temperature and charging range of users.

Aqueous Binders Compatible with Ionic Liquid Electrolyte for High-Performance Aluminum-Ion Batteries.

The incompatibility of poly(vinylidene difluoride) (PVDF) with acidic ionic liquid electrolytes and the use of toxic and high-cost N-methyl pyrrolidone (NMP) solvents hinder the wide application of aluminum-ion batteries (AIBs). In this work, sodium alginate (Na-Alg) is developed as an aqueous binder for the fabrication of graphite positive electrodes in AIBs. The compatibility of various binders with the ionic liquid electrolyte is evaluated, and interaction between various binders and graphite particles before and after cycling is compared and discussed. The results demonstrate that the well compatibility of Na-Alg in ionic liquids and its reasonable distribution on the graphite surface facilitate fast charge transfer and ion diffusion, reduce electrode polarization, and thus contributing to significantly improved cycling stability and rate capability of AIBs. This work provides a new insight into the development of low-cost, eco-friendly, and high-performance binders for AIBs.

Technical Note: Dosimetric feasibility of lattice radiotherapy for breast cancer using GammaPod.

PURPOSE: Studies on Lattice radiotherapy (LRT) for breast cancer have been largely lacking. This study investigates the dosimetric feasibility of using Gamma Pod, a stereotactic radiotherapy apparatus originally designed for breast SBRT, to deliver LRT to large, bulky breast tumor as a noninvasive treatment option. METHODS: The GammaPod-based LRT was simulated using Geant4 Gate Monte Carlo software. The simulated GammaPod was equipped with 5 mm diameter non-coplanar circular beams that span 28° latitudinally from 18° to 43° off the horizontal plane. Two degrees longitudinal intervals were used to simulate rotating sources. To simulate the treatments to different breast sizes, three water-equivalent hemisphere volumes with diameters of 10, 15, and 20 cm were analyzed. The lattice was planned by spacing focal points 2 cm apart in the transverse and sagittal planes and 2.5 cm in the coronal plane. This resulted in 22-172 shots for full breast treatment. The maximum dose for each individual shot was 20 Gy. The peak-to-valley dose differences and skin dose were analyzed. To verify the feasibility of delivering LRT, a test plan was created and delivered to a commercial diode array dose verification device using a clinical GammaPod system with 15 mm collimators. RESULTS: The dose profiles showed the average peak-to-valley dose percent differences of 94.10% in the 10 cm hemispherical volume, 88.95% in the 15 cm hemispherical volume, and 83.60% in the 20 cm hemispherical volume. Average skin dose was 1.27, 1.72, and 2.13 Gy for the 10, 15, and 20 cm irradiation volumes, respectively. The LRT plan delivered using a clinical GammaPod system with larger collimators verified the feasibility of LRT plan delivery. CONCLUSION: GammaPod-based lattice radiotherapy is a viable treatment option and its application can be extended to treating large bulky breast tumors.

Structure-guided DNA-DNA attraction mediated by divalent cations.

Probing the role of surface structure in electrostatic interactions, we report the first observation of sequence-dependent dsDNA condensation by divalent alkaline earth metal cations. Disparate behaviors were found between two repeating sequences with 100% AT content, a poly(A)-poly(T) duplex (AA-TT) and a poly(AT)-poly(TA) duplex (AT-TA). While AT-TA exhibits non-distinguishable behaviors from random-sequence genomic DNA, AA-TT condenses in all alkaline earth metal ions. We characterized these interactions experimentally and investigated the underlying principles using computer simulations. Both experiments and simulations demonstrate that AA-TT condensation is driven by non-specific ion-DNA interactions. Detailed analyses reveal sequence-enhanced major groove binding (SEGB) of point-charged alkali ions as the major difference between AA-TT and AT-TA, which originates from the continuous and close stacking of nucleobase partial charges. These SEGB cations elicit attraction via spatial juxtaposition with the phosphate backbone of neighboring helices, resulting in an azimuthal angular shift between apposing helices. Our study thus presents a distinct mechanism in which, sequence-directed surface motifs act with cations non-specifically to enact sequence-dependent behaviors. This physical insight allows a renewed understanding of the role of repeating sequences in genome organization and regulation and offers a facile approach for DNA technology to control the assembly process of nanostructures.

Additive Modulation of DNA-DNA Interactions by Interstitial Ions.

Quantitative understanding of biomolecular electrostatics, particularly involving multivalent ions and highly charged surfaces, remains lacking. Ion-modulated interactions between nucleic acids provide a model system in which electrostatics plays a dominant role. Using ordered DNA arrays neutralized by spherical cobalt3+ hexammine and Mg2+ ions, we investigate how the interstitial ions modulate DNA-DNA interactions. Using methods of ion counting, osmotic stress, and x-ray diffraction, we systematically determine thermodynamic quantities, including ion chemical potentials, ion partition, DNA osmotic pressure and force, and DNA-DNA spacing. Analyses of the multidimensional data provide quantitative insights into their interdependencies. The key finding of this study is that DNA-DNA forces are observed to linearly depend on the partition of interstitial ions, suggesting the dominant role of ion-DNA coupling. Further implications are discussed in light of physical theories of electrostatic interactions and like-charge attraction.

Study of the discharge/charge process of lithium-sulfur batteries by electrochemical impedance spectroscopy.

Electrochemical impedance spectroscopy (EIS) was used to study the initial discharge/charge process in a sulfur cathode with different potentials. In the second discharge region (2.00-1.70 V), where soluble polysulfides are reduced to Li2S, the EIS spectra exhibit three semicircles/arcs as the frequency decreased. An appropriate equivalent circuit is proposed to fit the experimental EIS data. Based on detailed analysis of the change in kinetic parameters obtained from simulating the experimental EIS data as functions of potential, the high-frequency, middle-frequency and low-frequency semicircles/arcs can be attributed to the Schottky contact reflecting the electronic properties of materials, the charge transfer step and the formation of Li2S respectively. The inclined line arises from the diffusion process in the detectable potentials and frequency range. Several important electrochemical reactions also have been verified by cyclic voltammetry curves.

Touch-Spun Nanofibers for Nerve Regeneration.

In the current study, we examined the potential for neural stem cell (NSCs) proliferation on novel aligned touch-spun polycaprolactone (PCL) nanofibers. Electrospun PCL nanofibers with similar diameter and alignment were used as a control. Confocal microscopy images showed that NSCs grew and differentiated all over the scaffolds up to 8 days. Neurite quantification analysis revealed that the NSCs cultured on the touch-spun fibers with incorporated bovine serum albumin promoted the expression of neuron-specific class III ß-tubulin after 8 days. More importantly, NSCs grown on the aligned touch-spun PCL fibers exhibited a bipolar elongation along the direction of the fiber, while NSCs cultured on the aligned electrospun PCL fibers expressed a multipolar elongation. The structural characteristics of the PCL nanofibers analyzed by X-ray diffraction indicated that the degree of crystallinity and elastic modulus of the touch-spun fiber are significantly higher than those of electrospun fibers. These findings indicate that the aligned and stiff touch-spun nanofibrous scaffolds show considerable potential for nerve injury repair.

Development of 3D printable conductive hydrogel with crystallized PEDOT:PSS for neural tissue engineering.

Bioelectronic devices enable efficient and effective communication between medical devices and human tissue in order to directly treat patients with various neurological disorders. Due to the mechanical similarity to human tissue, hydrogel-based electronic devices are considered to be promising for biological signal recording and stimulation of living tissues. Here, we report the first three-dimensionally (3D) printable conductive hydrogel that can be photocrosslinked while retaining high electrical conductivity. In addition, we prepared dorsal root ganglion (DRG) cell-encapsulated gelatin methacryloyl (GelMA) hydrogels which were integrated with the 3D printed conductive structure and evaluated for efficiency neural differentiation under electrical stimulation (ES). For enhanced electrical conductivity, a poly(3,4-ethylenedioxythiophene) (PEDOT): polystyrene sulfonate (PSS) aqueous solution was freeze-dried and mixed with polyethylene glycol diacrylate (PEGDA) as the photocurable polymer base. Next, the conductive hydrogel was patterned on the substrate by using a table-top stereolithography (SLA) 3D printer. The fabricated hydrogel was characterized for electrochemical conductivity. After printing with the PEDOT:PSS conductive solution, the patterned hydrogel exhibited decreased printing diameters with increasing of PEDOT:PSS concentration. Also, the resultant conductive hydrogel had significantly increased electrochemical properties with increasing PEDOT:PSS concentration. The 3D printed conductive hydrogel provides excellent structural support to systematically transfer the ES toward encapsulated DRG cells for enhanced neuronal differentiation. The results from this study indicate that the conductive hydrogel can be useful as a 3D printing material for electrical applications.

Combined Monte Carlo/torsion-angle molecular dynamics for ensemble modeling of proteins, nucleic acids and carbohydrates.

We describe a general method to use Monte Carlo simulation followed by torsion-angle molecular dynamics simulations to create ensembles of structures to model a wide variety of soft-matter biological systems. Our particular emphasis is focused on modeling low-resolution small-angle scattering and reflectivity structural data. We provide examples of this method applied to HIV-1 Gag protein and derived fragment proteins, TraI protein, linear B-DNA, a nucleosome core particle, and a glycosylated monoclonal antibody. This procedure will enable a large community of researchers to model low-resolution experimental data with greater accuracy by using robust physics based simulation and sampling methods which are a significant improvement over traditional methods used to interpret such data.

Monte Carlo simulation algorithm for B-DNA.

Understanding the structure-function relationship of biomolecules containing DNA has motivated experiments aimed at determining molecular structure using methods such as small-angle X-ray and neutron scattering (SAXS and SANS). SAXS and SANS are useful for determining macromolecular shape in solution, a process which benefits by using atomistic models that reproduce the scattering data. The variety of algorithms available for creating and modifying model DNA structures lack the ability to rapidly modify all-atom models to generate structure ensembles. This article describes a Monte Carlo algorithm for simulating DNA, not with the goal of predicting an equilibrium structure, but rather to generate an ensemble of plausible structures which can be filtered using experimental results to identify a sub-ensemble of conformations that reproduce the solution scattering of DNA macromolecules. The algorithm generates an ensemble of atomic structures through an iterative cycle in which B-DNA is represented using a wormlike bead-rod model, new configurations are generated by sampling bend and twist moves, then atomic detail is recovered by back mapping from the final coarse-grained configuration. Using this algorithm on commodity computing hardware, one can rapidly generate an ensemble of atomic level models, each model representing a physically realistic configuration that could be further studied using molecular dynamics. © 2016 Wiley Periodicals, Inc.

Ionic switch controls the DNA state in phage λ.

We have recently found that DNA packaged in phage λ undergoes a disordering transition triggered by temperature, which results in increased genome mobility. This solid-to-fluid like DNA transition markedly increases the number of infectious λ particles facilitating infection. However, the structural transition strongly depends on temperature and ionic conditions in the surrounding medium. Using titration microcalorimetry combined with solution X-ray scattering, we mapped both energetic and structural changes associated with transition of the encapsidated λ-DNA. Packaged DNA needs to reach a critical stress level in order for transition to occur. We varied the stress on DNA in the capsid by changing the temperature, packaged DNA length and ionic conditions. We found striking evidence that the intracapsid DNA transition is 'switched on' at the ionic conditions mimicking those in vivo and also at the physiologic temperature of infection at 37°C. This ion regulated on-off switch of packaged DNA mobility in turn affects viral replication. These results suggest a remarkable adaptation of phage λ to the environment of its host bacteria in the human gut. The metastable DNA state in the capsid provides a new paradigm for the physical evolution of viruses.

DNA under Force: Mechanics, Electrostatics, and Hydration.

Quantifying the basic intra- and inter-molecular forces of DNA has helped us to better understand and further predict the behavior of DNA. Single molecule technique elucidates the mechanics of DNA under applied external forces, sometimes under extreme forces. On the other hand, ensemble studies of DNA molecular force allow us to extend our understanding of DNA molecules under other forces such as electrostatic and hydration forces. Using a variety of techniques, we can have a comprehensive understanding of DNA molecular forces, which is crucial in unraveling the complex DNA functions in living cells as well as in designing a system that utilizes the unique properties of DNA in nanotechnology.

Capsules with a hierarchical shell structure assembled by aminoglycosides and DNA via the kinetic path.

Aminoglycosides are capable of expelling water molecules when forming a complex with DNA via electrostatic interaction. The "water-proof" nature of the complex leads to the formation of capsules, which possess hierarchical shell structures with a smooth and rigid outer layer and a viscoelastic inner layer.

Solution scattering and FRET studies on nucleosomes reveal DNA unwrapping effects of H3 and H4 tail removal.

Using a combination of small-angle X-ray scattering (SAXS) and fluorescence resonance energy transfer (FRET) measurements we have determined the role of the H3 and H4 histone tails, independently, in stabilizing the nucleosome DNA terminal ends from unwrapping from the nucleosome core. We have performed solution scattering experiments on recombinant wild-type, H3 and H4 tail-removed mutants and fit all scattering data with predictions from PDB models and compared these experiments to complementary DNA-end FRET experiments. Based on these combined SAXS and FRET studies, we find that while all nucleosomes exhibited DNA unwrapping, the extent of this unwrapping is increased for nucleosomes with the H3 tails removed but, surprisingly, decreased in nucleosomes with the H4 tails removed. Studies of salt concentration effects show a minimum amount of DNA unwrapping for all complexes around 50-100mM of monovalent ions. These data exhibit opposite roles for the positively-charged nucleosome tails, with the ability to decrease access (in the case of the H3 histone) or increase access (in the case of the H4 histone) to the DNA surrounding the nucleosome. In the range of salt concentrations studied (0-200mM KCl), the data point to the H4 tail-removed mutant at physiological (50-100mM) monovalent salt concentration as the mononucleosome with the least amount of DNA unwrapping.

Electrostatically driven interactions between hybrid DNA-carbon nanotubes.

Single-stranded DNA is able to wrap around single-wall carbon nanotubes (CNT) and form stable DNA-CNT hybrids that are highly soluble in solution. Here we report quantitative measurements and analysis of the interactions between DNA-CNT hybrids at low salts. Condensation of DNA-CNT hybrids by neutral osmolytes leads to liquid crystalline phases, and varying the osmotic pressure modulates the interhybrid distance that is determined by x-ray diffraction. Thus obtained force-distance dependencies of DNA-CNT hybrids show a remarkable resemblance to that of double-stranded DNA with differences that can be largely accounted for by their different diameters. This establishes their common physical nature of electrostatically driven interactions. Quantitative modeling further reveals the roles of hydration in mediating the interhybrid forces within the last nanometer of surface separation. This study also suggests the utility of osmotic pressure to control DNA-CNT assemblies at subnanometer precision.

Ion competition in condensed DNA arrays in the attractive regime.

Physical origin of DNA condensation by multivalent cations remains unsettled. Here, we report quantitative studies of how one DNA-condensing ion (Cobalt(3+) Hexammine, or Co(3+)Hex) and one nonDNA-condensing ion (Mg(2+)) compete within the interstitial space in spontaneously condensed DNA arrays. As the ion concentrations in the bath solution are systematically varied, the ion contents and DNA-DNA spacings of the DNA arrays are determined by atomic emission spectroscopy and x-ray diffraction, respectively. To gain quantitative insights, we first compare the experimentally determined ion contents with predictions from exact numerical calculations based on nonlinear Poisson-Boltzmann equations. Such calculations are shown to significantly underestimate the number of Co(3+)Hex ions, consistent with the deficiencies of nonlinear Poisson-Boltzmann approaches in describing multivalent cations. Upon increasing the concentration of Mg(2+), the Co(3+)Hex-condensed DNA array expands and eventually redissolves as a result of ion competition weakening DNA-DNA attraction. Although the DNA-DNA spacing depends on both Mg(2+) and Co(3+)Hex concentrations in the bath solution, it is observed that the spacing is largely determined by a single parameter of the DNA array, the fraction of DNA charges neutralized by Co(3+)Hex. It is also observed that only ∼20% DNA charge neutralization by Co(3+)Hex is necessary for spontaneous DNA condensation. We then show that the bath ion conditions can be reduced to one variable with a simplistic ion binding model, which is able to describe the variations of both ion contents and DNA-DNA spacings reasonably well. Finally, we discuss the implications on the nature of interstitial ions and cation-mediated DNA-DNA interactions.