Developing efficient deep learning model for predicting copolymer properties.

Deep learning models are gaining popularity and potency in predicting polymer properties. These models can be built using pre-existing data and are useful for the rapid prediction of polymer properties. However, the performance of a deep learning model is intricately connected to its topology and the volume of training data.

Molecular simulation of the shape deformation of a polymersome.

Vesicles composed of diblock copolymers, or polymersomes, have proven to possess numerous applications ranging from drug delivery to catalytically driven nano-motors. The shape of a polymersome can be responsive to external stimuli, such as light or solvent. Molecular dynamics simulations reveal that the shape change upon the contraction of the inner volume of a polymersome vesicle occurs in two separate regimes-a stretching regime and a bending regime.

Interaction of Camptothecin with Model Cellular Membranes.

Accurate and efficient prediction of drug partitioning in model membranes is of significant interest to the pharmaceutical industry. Herein, we utilize advanced sampling methods, specifically, the adaptive biasing force methodology to calculate the potential of mean force for a model hydrophobic anticancer drug, camptothecin (CPT), across three model interfaces. We consider an octanol bilayer, a thick octanol/water interface, and a model 1-palmitoyl-2-oleoyl--glycero-3-phosphocholine (POPC)/water interface.

Rational Coarse-Grained Molecular Dynamics Simulations of Supramolecular Anticancer Nanotubes.

Peptide self-assembly has been used to design an array of nanostructures that possess functional biomedical applications. Experimental studies have reported nanofilament and nanotube formation from peptide-based drug amphiphiles (DAs). These DAs have shown to possess an inherently high drug loading with a tunable release mechanism.

Molecular Mechanism for the Role of the H2A and H2B Histone Tails in Nucleosome Repositioning.

The nucleosome core particle (NCP) is the basic packaging unit of DNA. Recently reported structures of the NCP suggest that the histone octamer undergoes conformational changes during the process of DNA translocation around the histone octamer. Herein, we demonstrate with long-time all-atomistic molecular dynamics simulations that the histone tails play a critical role in this nucleosome repositioning.

Molecular Dynamics Simulations of Supramolecular Anticancer Nanotubes.

We report here on long-time all-atomistic molecular dynamics simulations of functional supramolecular nanotubes composed by the self-assembly of peptide-drug amphiphiles (DAs). These DAs have been shown to possess an inherently high drug loading of the hydrophobic anticancer drug camptothecin. We probe the self-assembly mechanism from random with ∼0.

Effect of Nucleotide State on the Protofilament Conformation of Tubulin Octamers.

At the molecular level, the dynamic instability (random growth and shrinkage) of the microtubule (MT) is driven by the nucleotide state (GTP vs GDP) in the β subunit of the tubulin dimers at the MT cap. Here, we use large-scale molecular dynamics (MD) simulations and normal-mode analysis (NMA) to characterize the effect of a single GTP cap layer on tubulin octamers composed of two neighboring protofilaments (PFs). We utilize recently reported high-resolution structures of dynamic MTs to simulate a GDP octamer both with and without a single GTP cap layer.

Glassy worm-like micelles in solvent and shear mediated shape transitions.

The glassiness of polymer melts is generally considered to be suppressed by small dimensions, added solvent, and heat. Here, we suggest that glassiness persists at the nanoscale in worm-like micelles composed of amphiphilic diblock copolymers of poly(ethylene oxide)-polystyrene (PS). The glassiness of these worms is indicated by a lack of fluorescence recovery after photobleaching as well as micron-length rigid segments separated by hinges.

Nanosensing of Pesticides by Zinc Oxide Quantum Dot: An Optical and Electrochemical Approach for the Detection of Pesticides in Water.

Present study reveals the low concentrations (∼4 ppm) of pesticide sensing vis-à-vis degradation of pesticides with the help of nontoxic zinc oxide quantum dots (QD). In our study, we have taken four different pesticides viz., aldrin, tetradifon, glyphosate, and atrazine, which are widely used in agriculture and have structural dissimilarities/diversity.

Microscopic understanding of the conformational features of a protein-DNA complex.

Protein-DNA interactions play crucial roles in different biological processes. Binding of a protein to its target DNA is the key step at different stages of genetic activities. In this article, we have carried out atomistic molecular dynamics simulations to understand the microscopic conformational and dynamical features of the N-terminal domain of the λ-repressor protein and its operator DNA in their complexed state.

Molecular simulations of peptide amphiphiles.

This review describes recent progress in the area of molecular simulations of peptide assemblies, including peptide-amphiphiles and drug-amphiphiles. The ability to predict the structure and stability of peptide self-assemblies from the molecular level up is vital to the field of nanobiotechnology. Computational methods such as molecular dynamics offer the opportunity to characterize intermolecular forces between peptide-amphiphiles that are critical to the self-assembly process.

Asymmetric breathing motions of nucleosomal DNA and the role of histone tails.

The most important packing unit of DNA in the eukaryotic cell is the nucleosome. It undergoes large-scale structural re-arrangements during different cell cycles. For example, the disassembly of the nucleosome is one of the key steps for DNA replication, whereas reassembly occurs after replication.

Exercise and eating habits among urban adolescents: a cross-sectional study in Kolkata, India.

Background: Unhealthy eating and lack of exercise during adolescence culminated into earlier onset and increasing burden of atherosclerotic cardiovascular diseases (CVDs) worldwide. Among urban Indian adolescents, prevalence of these risk factors of CVD seemed to be high, but data regarding their pattern and predictors was limited. To address this dearth of information, a survey was conducted among urban adolescent school-students in Kolkata, a highly populated metro city in eastern India.

Burden and Socio-Behavioral Correlates of Uncontrolled Abnormal Glucose Metabolism in an Urban Population of India.

Background: Progressive burden of diabetes mellitus is a major concern in India. Data on the predictors of poor glycemic control among diabetics are scanty. A population-based cross-sectional study nested in an urban cohort was thus conducted in West Bengal, India to determine the burden and correlates of total and uncontrolled abnormalities in glucose metabolism (AGM) in a representative population.

Thermodynamics of complex structures formed between single-stranded DNA oligomers and the KH domains of the far upstream element binding protein.

The noncovalent interaction between protein and DNA is responsible for regulating the genetic activities in living organisms. The most critical issue in this problem is to understand the underlying driving force for the formation and stability of the complex. To address this issue, we have performed atomistic molecular dynamics simulations of two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element binding protein (FBP) complexed with two single-stranded DNA (ss-DNA) oligomers in aqueous media.

Exploring ion induced folding of a single-stranded DNA oligomer from molecular simulation studies.

One crucial issue in DNA hydration is the effect of salts on its conformational features. This has relevance in biology as cations present in the cellular environment shield the negative charges on the DNA backbone, thereby reducing the repulsive force between them. By screening the negative charges along the backbone, cations stabilize the folded structure of DNA.

Effects of protein-DNA complex formation on the intermolecular vibrational density of states of interfacial water.

Single-stranded DNAs (ss-DNAs) are formed as intermediates during DNA metabolic processes. ss-DNA binding (SSB) proteins specifically bind to the single-stranded segments of the DNA and protect it from being degraded. We have performed room temperature molecular dynamics simulations of the aqueous solution of two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element (FUSE) binding protein (FBP) complexed with two ss-DNA oligomers.

Arbitrarily Long Relativistic Bit Commitment.

We consider the recent relativistic bit commitment protocol introduced by Lunghi et al. [Phys. Rev.

Dynamics of water around the complex structures formed between the KH domains of far upstream element binding protein and single-stranded DNA molecules.

Single-stranded DNA (ss-DNA) binding proteins specifically bind to the single-stranded regions of the DNA and protect it from premature annealing, thereby stabilizing the DNA structure. We have carried out atomistic molecular dynamics simulations of the aqueous solutions of two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element binding protein complexed with two short ss-DNA segments. Attempts have been made to explore the influence of the formation of such complex structures on the microscopic dynamics and hydrogen bond properties of the interfacial water molecules.

Correlated Conformational Motions of the KH Domains of Far Upstream Element Binding Protein Complexed with Single-Stranded DNA Oligomers.

Single-stranded DNA binding (SSB) proteins bind with single-stranded DNA (ss-DNA) segments that are generated as intermediates during DNA metabolic processes. The primary function of an SSB protein is to protect the ss-DNA from being degraded so that other enzymes can effectively act on it. We have performed atomistic molecular dynamics simulations of the two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element (FUSE) binding protein (FBP) complexed with two ss-DNA oligomers in aqueous solutions.

Microscopic dynamics of water around unfolded structures of barstar at room temperature.

The breaking of the native structure of a protein and its influences on the dynamic response of the surrounding solvent is an important issue in protein folding. In this work, we have carried out atomistic molecular dynamics simulations to unfold the protein barstar at two different temperatures (400 K and 450 K). The two unfolded forms obtained at such high temperatures are further studied at room temperature to explore the effects of nonuniform unfolding of the protein secondary structures along two different pathways on the microscopic dynamical properties of the surface water molecules.

Effect of temperature on the low-frequency vibrational spectrum and relative structuring of hydration water around a single-stranded DNA.

Molecular dynamics simulations of the single-stranded DNA oligomer (5'-CGCGAAT TCGCG-3') in aqueous solution have been carried out at different temperatures between 160 K and 300 K. The effects of temperature on the low-frequency vibrational spectrum and local structural arrangements of water molecules hydrating the DNA strand have been explored in detail. The low-frequency density of states distributions reveal that increasingly trapped transverse water motions play a dominant role in controlling the band corresponding to O⋯O⋯O bending or transverse oscillations of hydration water at supercooled temperatures.

Correlated dynamical crossovers of the hydration layer of a single-stranded DNA oligomer.

Atomistic molecular dynamics (MD) simulations at different temperatures ranging from 160 to 300 K have been carried out to explore the correlated dynamical transitions of a single-stranded DNA (ss-DNA) oligomer with heterogeneous distribution of nucleobases, 5'-CGCGAATTCGCG-3', and that of its hydration water. The calculations reveal a distinct dynamical crossover of the DNA oligomer associated with abrupt changes of motions of its atoms at around 200-220 K. Importantly, it is found from calculated water diffusivities and relaxation times that the hydration water molecules also exhibit a crossover within 210-220 K.

Molecular dynamics simulation of a single-stranded DNA with heterogeneous distribution of nucleobases in aqueous medium.

The DNA metabolic processes often involve single-stranded DNA (ss-DNA) molecules as important intermediates. In the absence of base complementarity, ss-DNAs are more flexible and interact strongly with water in aqueous media. Ss-DNA-water interactions are expected to control the conformational flexibility of the DNA strand, which in turn should influence the properties of the surrounding water molecules.