Evidence of vacancy ordered structures in PuO2-x and AmO2-x from first-principles calculations.

A combination of first-principles calculations and cluster expansion method is used to study ordering of oxygen vacancies in PuO2-x and AmO2-x. Vacancy ordered stable/metastable structures of composition Pu8O15 (PuO1.875), Pu6O11 (PuO1.833), Pu8O14 (PuO1.75) and Am10O19 (AmO1.90), Am8O15 (AmO1.875), Am10O18 (AmO1.80), Am8O13 (AmO1.625) are identified in PuO2-x and AmO2-x, respectively, from cluster expansion calculations. A comparison of formation enthalpies of vacancy ordered and vacancy disordered structures shows that Am8O15 (AmO1.875) and Am8O13 (AmO1.625) are more stable by 52 and 55 meV per atom, respectively, compared to their disordered counterparts. Similarly, vacancy ordered Pu8O15 (PuO1.875) and Pu8O14 (PuO1.75) structures are more stable compared to the disordered structures by 10 and 8 meV per atom, respectively. In contrast, the disordered PuO1.625 structure is more stable compared to the cluster expansion generated structures. The vacancy ordered structures are mechanically stable and their bulk modulus, Young's modulus, shear modulus and Poisson's ratio are reported.

Defect properties and solution energies of dopants in NASICON-type LiGe2(PO4)3 solid electrolyte: a first-principles study.

NASICON-type solid electrolytes are suitable choices for solid state batteries considering safer and more stable electrochemical performance compared to other potential solid electrolytes. The present study investigates intrinsic defects and dopant incorporation energetics in the LiGe2(PO4)3 (LGP) electrode material using density functional theory-based calculations. The formation energies of intrinsic defects (Frenkel, Schottky and anti-sites) indicate that Li Frenkel pair formation is the most energetically feasible process. With an aim to improve the lithium ion conductivity and chemical stability by suitable doping, solution energies are calculated for various trivalent (M3+ = B3+, Al3+, Ga3+, Sc3+, In3+, Y3+, Gd3+, La3+) and tetravalent (M4+ = Si4+, Ti4+, Sn4+ and Zr4+) ions substituted at the Ge4+ site. The most favourable trivalent and tetravalent dopants are Al3+ and Ti4+, respectively. The changes in lattice parameters with doping are correlated with channel/bottleneck size for Li+ migration. Alkali atom doping at the Li+ site is energetically favourable whereas alkali-earth doping at the Li+ site is not. Analysis based on Bader charges and density of states delineates changes in chemical interactions between the dopant atoms and the host LGP.

First-principles property assessment of hybrid formate perovskites.

Hybrid organic-inorganic formate perovskites, AB(HCOO)3, are a large family of compounds that exhibit a variety of phase transitions and diverse properties, such as (anti)ferroelectricity, ferroelasticity, (anti)ferromagnetism, and multiferroism. While many properties of these materials have already been characterized, we are not aware of any study that focuses on the comprehensive property assessment of a large number of formate perovskites. A comparison of the properties of materials within the family is challenging due to systematic errors attributed to different techniques or the lack of data. For example, complete piezoelectric, dielectric, and elastic tensors are not available. In this work, we utilize first-principles density functional theory based simulations to overcome these challenges and to report structural, mechanical, dielectric, piezoelectric, and ferroelectric properties of 29 formate perovskites. We find that these materials exhibit elastic stiffness in the range 0.5-127.0 GPa; highly anisotropic linear compressibility, including zero and even negative values; dielectric constants in the range 0.1-102.1; highly anisotropic piezoelectric response with the longitudinal values in the range 1.18-21.12 pC/N; and spontaneous polarizations in the range 0.2-7.8 µC/cm2. Furthermore, we propose and computationally characterize a few formate perovskites that have not been reported yet.

Unusual Properties of Hydrogen-Bonded Ferroelectrics: The Case of Cobalt Formate.

Hybrid organic-inorganic perovskites is a class of materials with diverse chemically tunable properties and outstanding potential for multifunctionality. We use first-principles simulations to predict room temperature ferroelectricity in a representative of the formate family, [NH_{2}NH_{3}][Co(HCOO)_{3}]. The ferroelectricity arises as a "by-product" of structural transition driven by the stabilization of the hydrogen bond. As a consequence the coupling with the electric field is relatively weak giving origin to large intrinsic coercive fields and making material immune to the depolarizing fields known for its detrimental role in nanoscale ferroelectrics. Insensitivity to the electric field and the intrinsic dynamics of the order-disorder transition in such material leads to the supercoercivity defined as significant increase in the coercive field with frequency. Room temperature polarization measurements provide further support for the predictions.

A Network Thermodynamic Analysis of Amyloid Aggregation along Competing Pathways.

Aggregation of proteins towards amyloid formation is a significant event in many neurodegenerative diseases. Low-molecular weight oligomers are considered to be the primary toxic agents in many of these maladies. Therefore, there is an increasing interest in understanding their formation and behavior. In this paper, we build on our previously established theoretical investigations on the interactions between Aß and lipids (L) that adopt off-pathway fibril formation under the control of L concentrations. Our previously developed competing game theoretic framework between the on- and off-pathway dynamics has been expanded to understand the underlying network topological structures in the reaction kinetics of amyloid formation. The mass-action based dynamical systems are solved to identify dominant pathways in the system with fixed initial conditions, and variations in the occurrence of these dominant pathways are identified as a function of various seeding conditions. The mechanistic approach is supported by thermodynamic free energy computations which helps identify stable reactions. The resulting analysis provides possible intervention strategies that can draw the dynamics away from the off-pathways and potential toxic intermediates. We also draw upon the classic literature on network thermodynamics to suggest new approaches to better understand such complex systems.

Phase Switching as the Origin of Large Piezoelectric Response in Organic-Inorganic Perovskites: A First-Principles Study.

Piezoelectrics are critical functional components of many practical applications such as sensors, ultrasonic transducers, actuators, medical imaging, and telecommunications. So far, the best performing piezoelectrics are ferroelectric ceramics, many of which are toxic, heavy, hard, and cost-ineffective. Recently, a groundbreaking discovery of extraordinarily large piezoelectric coefficients in the family of organic-inorganic perovskites gave a hope for a cheaper, environmentally friendly, inexpensive, lightweight, and flexible alternative. However, the origin of such a response in organic-inorganic ferroelectrics whose spontaneous polarization is an order of magnitude smaller than for inorganic counterparts remains unclear. In our study, we employ first-principles simulations to predict that the mechanism associated with large piezoelectric constants is of extrinsic origin and associated with switching between the stable phase and a previously overlooked energetically competitive metastable phase that can be stabilized by the external stress. The phase switching changes the polarization direction and therefore produces a large piezoelectric response similar to PbZr_{1-x}Ti_{x}O_{3} near the morphotropic phase boundary. The existence of such metastable phases is likely to manifest as the dynamical molecular disorder above the Curie temperature and therefore could be intrinsic to the entire family of organic-inorganic ferroelectrics with such disorder.

Structural, thermodynamic, electronic and elastic properties of Th1-xUxO2 and Th1-xPuxO2 mixed oxides.

The structural, thermodynamic, electronic, and elastic properties of Th1-xUxO2 and Th1-xPuxO2 mixed oxides (MOX) have been calculated with Hubbard corrected density functional theory (DFT+U) to account for the strong 5f electron correlations. The ideal solid solution is approximated by special quasi-random structures and the U-ramping method is used to account for the presence of metastable states in the self-consistent field solution of the DFT+U approach. The mixing enthalpy (ΔHmix) is positive throughout the composition range of the Th1-xUxO2 MOX, consistent with a simple miscibility gap (at low temperature) phase diagram. The behavior of the Th1-xPuxO2 MOX is more complex, where ΔHmix is positive in the ThO2-rich region and negative in the PuO2-rich region. Electronic structure analysis shows that substitution of Th by U/Pu in ThO2 leads to a reduction of the average Th-O bond lengths, causing distortion in the crystal structure. The distortion in the crystal structure results in an increase in the conduction bandwidth and a reduction of the band-gap in the MOX. Good agreement of our DFT+U calculated elastic properties of ThO2, UO2 and PuO2 compounds with experiments leads to convincing prediction of these properties for Th1-xUxO2 and Th1-xPuxO2 MOX.

First-principles study of phase stability, electronic and mechanical properties of plutonium sub-oxides.

The formation energies (ΔHf) of fluorite PuO2, α-Pu2O3 and sub-oxides PuO2-x (0.0 < x < 0.5) are determined from atomic scale simulations based on density functional theory (DFT) employing the generalised gradient approximation (GGA) corrected with an effective Hubbard parameter (Ueff). The variation of structural and electronic properties of PuO2 and α-Pu2O3 is determined while ramping up Ueff from 0 eV to 5 eV (Ueff-ramping method) to treat the presence of metastable magnetic states and to determine the most suitable Ueff value matching the experiments. The GGA+U calculated lattice parameter variation as a function of stoichiometry (a(x)) for PuO2-x shows a positive volume of relaxation and an almost linear variation presented by the relation a(x) = a0- 0.522738x, where a0 is the equilibrium lattice parameter of PuO2. The GGA+U calculated ΔHf values of PuO2-x lie above the tie line connecting the ΔHf of PuO2 and Pu2O3, and with decreasing O/Pu ratio, the stability of the sub-oxides increases. The crystal and electronic structure analysis of the oxygen vacancy in PuO2 shows outward anisotropic relaxation of four Pu atoms around the vacancy site. The electronic charges within the Wigner-Seitz sphere around these Pu atoms show an overall gain of only (0.12-0.22)e per Pu atom, signifying an incomplete localization of charges. Finally, the GGA+U calculated single crystal elastic constant values decrease continuously with decreasing O/Pu ratio from 2.0 to 1.5. The rate of decrease of the average C11 is almost 11-15 times higher compared to the rate of decrease of C12 and C44.

Association and expression of the antigen-processing gene PSMB8, coding for low-molecular-mass protease 7, with vitiligo in North India: case-control study.

BACKGROUND: Vitiligo is a multifactorial, autoimmune, depigmenting disorder of the skin where aberrant presentation of autoantigens may have a role. OBJECTIVES: To study the association of two antigen-processing genes, PSMB8 and PSMB9, with vitiligo. METHODS: In total 1320 cases of vitiligo (1050 generalized and 270 localized) and 752 healthy controls were studied for the PSMB9 exon 3 G/A single-nucleotide polymorphism (SNP), PSMB8 exon 2 C/A SNP and PSMB8 intron 6 G/T SNP at site 37 360 using polymerase chain reaction (PCR)-restriction fragment length polymorphism. Real-time PCR was used for transcriptional expression of PSMB8 and cytokines. Expression of ubiquitinated proteins and phosphorylated-p38 (P-p38) was studied by Western blotting. RESULTS: Significant increases in PSMB8 exon 2 allele A (P < 2.07 × 10-6 , odds ratio 1·93) and genotypes AA (P < 1.03 × 10-6 , odds ratio 2·51) and AC (P < 1.29 × 10-6 , odds ratio 1·63) were observed in patients with vitiligo. Interferon-γ stimulation induced lower expression of PSMB8 in peripheral blood mononuclear cells of cases compared with controls, suggesting impaired antigen processing, which was confirmed by accumulation of ubiquitinated proteins in both lesional and nonlesional skin of patients with vitiligo. Expression of proinflammatory cytokines - interleukin (IL)-6, IL-1ß and IL-8 - was higher in the lesional skin. P-p38 expression was variable but correlated with the amount of ubiquitinated proteins in the lesional and nonlesional skin, suggesting that the inflammatory cytokine responses in lesional skin could be a result of both P-p38-dependent and -independent pathways. CONCLUSIONS: The PSMB8 exon 2 SNP is significantly associated with vitiligo. Accumulation of ubiquitinated proteins in skin of cases of vitiligo suggests their aberrant processing, which may promote the development of the disease.

A computational study of high pressure polymorphic transformations in monazite-type LaPO4.

Polymorphic transformations in LaPO4 are investigated as a function of pressure using density functional theory (DFT) based calculations under the generalized gradient approximation. The monazite-type (P21/n) → barite-type (Pbnm) structural transformation is identified at 16.2 GPa and experimentally, no transformation is observed near this pressure. A discontinuity in the pressure-volume relation (of 4.16% volume discontinuity compared to the monazite structure at the same pressure) and unit-cell dimensions is observed around 28 GPa, which matches well with the previous experimental results. The pressure of discontinuity matches the DFT calculated monazite-type (P21/n) → post barite-type (P212121) structural transformation pressure. The equation of state, single crystal elastic constants and phonon dispersion curves of the different polymorphs as a function of pressure are determined. Both the barite-type (Pbnm) and post barite-type (P212121) structures are mechanically and dynamically stable at 27 GPa indicating that the monazite-type (P21/n) → barite-type (Pbnm) phase transformation may be hindered by a kinetic barrier. The phase transformation in monazite-type LaPO4 is driven by a softening of the C25 single crystal elastic constant. Moreover, a small displacement and tilting of PO4 tetrahedra as a function of pressure leads to a change in the La chemical environment and creates space for the construction of LaO12 polyhedra from LaO9 due to a phase transformation.

Phase stability, electronic structures and elastic properties of (U,Np)O2 and (Th,Np)O2 mixed oxides.

Mixing enthalpies (ΔHmix) of U1-xNpxO2 and Th1-xNpxO2 solid solutions are derived from atomic scale simulations based on density functional theory (DFT) employing the generalised gradient approximation corrected with an effective Hubbard parameter (Ueff). The variation of structural and electronic properties of UO2 and NpO2 with collinear ferromagnetic (FM), collinear anti-ferromagnetic (AFM) and non-collinear anti-ferromagnetic arrangements of the uranium and neptunium magnetic moments are investigated while ramping up Ueff from 0 eV to 4 eV (the Ueff-ramping method). A combination of the Ueff-ramping method to treat the presence of metastable magnetic states and special-quasirandom structures (SQS) for the random distribution of Np atoms in UO2 and ThO2 is employed to calculate ΔHmix of U1-xNpxO2 and Th1-xNpxO2 mixed oxides (MOX). The effect of collinear FM and AFM ordering is also considered in determining the ΔHmix. The calculated ΔHmix of Th1-xNpxO2 MOX were positive compared to the end members and nearly symmetric around x = 0.5 and ΔHmix of the AFM configuration were higher compared to the FM configuration maximum by 0.19 kJ mol-1. The ΔHmix of U1-xNpxO2 MOX were negative up to U0.50Np0.50O2 with a maximum value of -1.21 kJ mol-1 for U0.4375Np0.5625O2 whereas Np-rich (U,Np)O2 MOX compositions exhibited ΔHmix close to zero. Values of ΔHmix for (Th,Np)O2 are consistent with a simple miscibility-gap phase diagram while those for (U,Np)O2 suggest more complex behaviour. Nevertheless, lattice parameter variation with composition still follows a Vegard's law relationship. Finally, single crystal elastic constants of pure oxides and MOX are reported. The linear-elasticity models describe the mixing energies to within an accuracy of approximately 1 kJ mol-1 for the U1-xNpxO2 and Th1-xNpxO2 MOX systems.

Defect induced ferromagnetism in MgO and its exceptional enhancement upon thermal annealing: a case of transformation of various defect states.

MgO particles of few micron size are synthesized through a sol-gel method at different annealing temperatures such as 600 °C (MgO-600), 800 °C (MgO-800) and 1000 °C (MgO-1000). EDX and ICP-AES studies confirmed a near total purity of the sample with respect to paramagnetic metal ion impurities. Magnetic measurements showed a low temperature weak ferromagnetic ordering with a TC (Curie temperature) around 65 K (±5 K). Unexpectedly, the saturation magnetization (Ms) was found to be increased with increasing annealing temperature during synthesis. It was observed that with J = 1 or 3/2 or S = 1 or 3/2, the experimental points are fitted well with the Brillouin function of weak ferromagnetic ordering. A positron annihilation lifetime measurement study indicated the presence of a divacancy (2VMg + 2VO) cluster in the case of the low temperature annealed compound, which underwent dissociations into isolated monovacancies of Mg and O at higher annealing temperatures. An EPR study showed that both singly charged Mg vacancies and oxygen vacancies are responsible for ferromagnetic ordering. It also showed that at lower annealing temperatures the contribution from was very low while at higher annealing temperatures, it increased significantly. A PL study showed that most of the F+ centers were present in their dimer form, i.e. as centers. DFT calculation implied that this dimer form has a higher magnetic moment than the monomer. After a careful consideration of all these observations, which have been reported for the first time, this thermally tunable unusual magnetism phenomenon was attributed to a transformation mechanism of one kind of cluster vacancy to another.

A computational study on the superionic behaviour of ThO2.

This study reports the density functional theory (DFT) and classical molecular dynamics (MD) study of the lattice dynamical, mechanical and anionic transport behaviours of ThO2 in the superionic state. DFT calculations of phonon frequencies were performed at different levels of approximation as a function of isotropic dilation (ε) in the lattice parameter. With the expansion of the lattice parameter, there is a softening of B1u and Eu phonon modes at the X symmetry point of the Brillouin zone. As a result of the nonlinear decrease at the X point, the B1u and Eu phonon modes cross each other at ε = 0.03, which is associated with a sharp increase in the narrow peak of the phonon density of states, signifying a higher occupation and hence a higher coupling of these modes at high temperatures. The mode crossing also indicates anionic conductivity in the 〈001〉 direction leading to occupation of interstitial sites. Moreover, MD and nudged elastic band calculated diffusion barriers indicate that 〈001〉 is the easy direction for anion migration in the normal and superionic states. With a further increase in the lattice parameter, the B1u mode continues to soften and becomes imaginary at a strain (ε) of 0.036 corresponding to a temperature of 3430 K. The calculated temperature variation of single crystal elastic constants shows that the fluorite phase of ThO2 remains elastically stable up to the superionic regime, though the B1u phonon mode is imaginary in that state. This leads to anionic disorder at elevated temperatures. Tracking of anion positions in the superionic state as a function of time in MD simulations suggests a hopping model in which the oxygen ions migrate from one tetrahedral site to another via octahedral interstitial sites.

In silico characterization of 1,2-diacylglycerol cholinephosphotransferase and lysophospha-tidylcholine acyltransferase genes in Glycine max L. Merrill.

The enzymes 1,2-diacylglycerol cholinephosphotrans-ferase (CPT) and lysophosphatidylcholine acyltransferase (LPCAT) are important in lipid metabolism in soybean seeds. Thus, understand-ing the genes that encode these enzymes may enable their modification and aid the improvement of soybean oil quality. In soybean, the genes encoding these enzymes have not been completely described; there-fore, this study aimed to identify, characterize, and analyze the in silico expression of these genes in soybean. We identified two gene models encoding CPT and two gene models encoding LPCAT, one of which presented an alternative transcript. The sequences were positioned on the physical map of soybean and the promoter regions were analyzed. Cis-elements responsible for seed-specific expression and responses to biotic and abiotic stresses were identified. Virtual expression analysis of the gene models for CPT and LPCAT indicated that these genes are expressed under different stress conditions, in somatic embryos during differentiation, in immature seeds, root tissues, and calli. Putative ami-no acid sequences revealed the presence of transmembrane domains, and analysis of the cellular localization of these enzymes revealed they are located in the endoplasmic reticulum.

Temporal macrodynamics and microdynamics of the postoperative impedance at the tissue-electrode interface in deep brain stimulation patients.

OBJECTIVE: To study the temporal dynamics of tissue impedance after deep brain stimulation (DBS). BACKGROUND: DBS therapy commonly employs a constant voltage approach, and current delivery to the tissue is a function of electrode-tissue impedance. It is presumed that impedance fluctuates early postimplantation, with implications for variations in current delivery and therapeutic efficacy. We hypothesised that the largest variation will be recorded early after surgery, followed by stabilisation. METHODS: Review of impedance checks of implanted DBS systems at standard parameters during the first five months postimplantation. All measurement time points were binned into 1-week periods, and we used repeated measures analysis of variance with Tukey pairwise multiple comparisons correction. The analysis was repeated after normalising impedance values for each subject to that patient's baseline value. RESULTS: There was an initial (non-significant) drop in impedance at week 1, followed by significant increase at week 3 (p=0.0002). There were no further significant differences in impedance values at subsequent time points. Analysis of normalised data showed a significant difference between the initial measurement in postoperative week 1 (normalised value 1) and week 3 (normalised value 1.73, p<0.0001), with no further difference among the subsequent weekly points during the 5-month follow-up. No significant hourly variations were found at any time points. CONCLUSIONS: We found major changes in impedance within the first month postimplantation, with no further variation. This is an important confirmation in patients of this temporal dynamics of the impedance of implanted DBS hardware, with potential therapeutic implications.

Potential contribution of monoamine oxidase a gene variants in ADHD and behavioral co-morbidities: scenario in eastern Indian probands.

Attention deficit hyperactivity disorder (ADHD) is the most frequently diagnosed behavioral disorder in children with a high frequency of co-morbid conditions like conduct disorder (CD) and oppositional defiant disorder (ODD). These traits are controlled by neurotransmitters like dopamine, serotonin and norepinephrine. Monoamine oxidase A (MAOA), a mitochondrial enzyme involved in the degradation of amines, has been reported to be associated with aggression, impulsivity, depression, and mood changes. We hypothesized that MAOA can have a potential role in ADHD associated CD/ODD and analyzed 24 markers in a group of Indo-Caucasoid subjects. ADHD probands and controls (N = 150 each) matched for ethnicity and gender were recruited following the Diagnostic and Statistical Manual for Mental Disorders-IV. Appropriate scales were used for measuring CD and ODD traits. Markers were genotyped by PCR-based methods and data obtained analyzed using the Cocaphase program under UNPHASED. Only eight markers were found to be polymorphic. rs6323 "G" allele showed higher frequencies in ADHD (P = 0.0023), ADHD + CD (P = 0.03) and ADHD + ODD (P = 0.01) as compared to controls. Haplotype analysis revealed statistically significant difference for three haplotypes in ADHD cases (P < 0.02). Statistically significant differences were also noticed for haplotypes in ADHD + CD and ADHD + ODD cases (P < 0.01). LD analysis showed significant variation in different groups. Multidimensionality reduction analysis showed independent as well as interactive effects of markers. Genotypes showed correlation with behavioral problems in ADHD and ADHD + CD. We interpret that MAOA gene variants may contribute to the etiology of ADHD as well as associated co-morbid CD and ODD in this ethnic group.

A preliminary report on the genetic variation in pointed gourd (Trichosanthes dioica Roxb.) as assessed by random amplified polymorphic DNA.

Pointed gourd (Trichosanthes dioica Roxb.) is an economically important cucurbit and is extensively propagated through vegetative means, viz vine and root cuttings. As the accessions are poorly characterized it is important at the beginning of a breeding programme to discriminate among available genotypes to establish the level of genetic diversity. The genetic diversity of 10 pointed gourd races, referred to as accessions was evaluated. DNA profiling was generated using 10 sequence independent RAPD markers. A total of 58 scorable loci were observed out of which 18 (31.03%) loci were considered polymorphic. Genetic diversity parameters [average and effective number of alleles, Shannon's index, percent polymorphism, Nei's gene diversity, polymorphic information content (PIC)] for RAPD along with UPGMA clustering based on Jaccard's coefficient were estimated. The UPGMA dendogram constructed based on RAPD analysis in 10 pointed gourd accessions were found to be grouped in a single cluster and may represent members of one heterotic group. RAPD analysis showed promise as an effective tool in estimating genetic polymorphism in different accessions of pointed gourd.

PANNOTATOR: an automated tool for annotation of pan-genomes.

Due to next-generation sequence technologies, sequencing of bacterial genomes is no longer one of the main bottlenecks in bacterial research and the number of new genomes deposited in public databases continues to increase at an accelerating rate. Among these new genomes, several belong to the same species and were generated for pan-genomic studies. A pan-genomic study allows investigation of strain phenotypic differences based on genotypic differences. Along with a need for good assembly quality, it is also fundamental to guarantee good functional genome annotation of the different strains. In order to ensure quality and standards for functional genome annotation among different strains, we developed and made available PANNOTATOR (http://bnet.egr.vcu.edu/iioab/agenote.php), a web-based automated pipeline for the annotation of closely related and well-suited genomes for pan-genome studies, aiming at reducing the manual work to generate reports and corrections of various genome strains. PANNOTATOR achieved 98 and 76% of correctness for gene name and function, respectively, as result of an annotation transfer, with a similarity cut-off of 70%, compared with a gold standard annotation for the same species. These results surpassed the RAST and BASys softwares by 41 and 21% and 66 and 17% for gene name and function annotation, respectively, when there were reliable genome annotations of closely related species. PANNOTATOR provides fast and reliable pan-genome annotation; thereby allowing us to maintain the research focus on the main genotype differences between strains.

Stability analysis of 4-species Aß aggregation model: A novel approach to obtaining physically meaningful rate constants.

Protein misfolding and concomitant aggregation towards amyloid formation is the underlying biochemical commonality among a wide range of human pathologies. Amyloid formation involves the conversion of proteins from their native monomeric states (intrinsically disordered or globular) to well-organized, fibrillar aggregates in a nucleation-dependent manner. Understanding the mechanism of aggregation is important not only to gain better insight into amyloid pathology but also to simulate and predict molecular pathways. One of the main impediments in doing so is the stochastic nature of interactions that impedes thorough experimental characterization and the development of meaningful insights. In this study, we have utilized a well-known intermediate state along the amyloid-ß peptide aggregation pathway called protofibrils as a model system to investigate the molecular mechanisms by which they form fibrils using stability and perturbation analysis. Investigation of protofibril aggregation mechanism limits both the number of species to be modeled (monomers, and protofibrils), as well as the reactions to two (elongation by monomer addition, and protofibril-protofibril lateral association). Our new model is a reduced order four species model grounded in mass action kinetics. Our prior study required 3200 reactions, which makes determining the reaction parameters prohibitively difficult. Using this model, along with a linear perturbation argument, we rigorously determine stable ranges of rate constants for the reactions and ensure they are physically meaningful. This was accomplished by finding the ranges in which the perturbations dieout in a five-parameter sweep, which includes the monomer and protofibril equilibrium concentrations and three of the rate constants. The results presented are a proof-of-concept method in determining meaningful rate constants that can be used as a bonafide way for determining accurate rate constants for other models involving complex biological reactions such as amyloid aggregation.

Neurodegeneration and epigenetics: A review.

Neuronal function and differentiation are tightly regulated by both genome and epigenome. Based on the environmental information the epigenetic changes occur. Neurodegeneration is the consequence of dysregulation of both the genome and epigenome. In this study, we saw different types of alterations of epigenome present in neuronal cells of different model organisms for neurodegenerative disorders. The epigenetic modifications including chromatin modification, DNA methylation, and changes in regulatory RNAs (miRNA) are having a great impact on neurodegenerative disorders as well as memory. The effects of these re-editing in the neuronal cells cause Alzheimer's disease, Parkinson's disease, Huntington's disease but an unusual form of neuroepigenetics has been seen in Prion Disease. Subsequently, for the development of treatment of these diseases, epigenetic modifications should be kept in mind. Although until now many reports came on drug discovery inhibiting histone deacetylases and DNA methyltransferases to reverse the epigenetic change but they lack targeted delivery and sometimes cause a cytotoxic effect on neuronal cells. In future, advancement in targeted and non-cytotoxic drugs should be the main focus for therapeutic treatment of the neurodegenerative disorders.