molecular dynamics

The impact of a varied sulfur oxidation state (sulfide, sulfoxide, and sulfone) on imine dynamic covalent chemistry is presented. The role of noncovalent interactions, including chalcogen bonds and CH hydrogen bonds, on aldehyde/imine structures and imine exchange reactions was elucidated through experimental and computational evidence. The change in the sulfur oxidation state and diamine linkage further allowed the regulation of imine macrocycles, providing a platform for controlling molecular assemblies.

A series of atomistic molecular dynamics (MD) simulations were carried out with a hydrated 1,2-dimyristoyl- sn -glycero-3-phosphocholine (DMPC) bilayer with the variation of glucose concentrations from 0 to 30 wt % in the presence of 0.3 M NaCl. The study suggested that although the thickness of the lipid bilayer dropped significantly with the increase in glucose concentration, it expanded laterally at high glucose levels due to the intercalation of glucose between the headgroups of adjacent lipids. We adopted the surface assessment via the grid evaluation method to compute the deviation of the bilayer's key structural features for the different amounts of glucose present...

In this work, the <mml:math xmlns:mml="https://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>Crystal</mml:mi></mml:mrow> </mml:math>  code, developed previously by the authors to find "holes" as well as legitimate transition states in existing potential energy surface (PES) functions [JPC Lett. 11, 6468 (2020)], is retooled to perform on-the-fly "direct dynamics"-type PES explorations, as well as automatic construction of new PES functions. In all of these contexts, the chief advantage of <mml:math xmlns:mml="https://www...

Clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing is evolving into an essential tool in the field of biological and medical research. Notably, the development of catalytically deactivated Cas9 (dCas9) enzyme has substantially broadened its traditional boundaries in gene editing or perturbation. The conjugation of dCas9 with various molecular effectors allows precise control over transcriptional processes, epigenetic modifications, visualization of chromosomal dynamics, and several other applications...

CONTEXT: Further understanding of the molecular mechanisms is necessary since it is important for designing new drugs. This study aimed to understand the molecular mechanisms involved in the design of drugs that are inhibitors of the α-glucosidase enzyme. This research aims to gain further understanding of the molecular mechanisms underlying antidiabetic drug design. The molecular docking process yielded 4 compounds with the best affinity energy, including γ-Mangostin, 1,6-dimethyl-ester-3-isomangostin, 1,3,6-trimethyl-ester-α-mangostin, and 3,6,7-trimethyl-ester-γ-mangostin...

Cholesterol-rich lipid rafts are found to facilitate membrane fusion, central to processes like viral entry, fertilization, and neurotransmitter release. While the fusion process involves local, transient membrane dehydration, the impact of reduced hydration on cholesterol's structural organization in biological membranes remains unclear. Here, we employ confocal fluorescence microscopy and atomistic molecular dynamics simulations to investigate cholesterol behavior in phase-separated lipid bilayers under controlled hydration...

Recent experimental findings reveal nonconventional fluorescence emission in biological systems devoid of conjugated bonds or aromatic compounds, termed non-aromatic fluorescence (NAF). This phenomenon is exclusive to aggregated or solid states and remains absent in monomeric solutions. Previous studies focused on small model systems in vacuum show that the carbonyl stretching mode along with strong interaction of short hydrogen bonds (SHBs) remains the primary vibrational mode explaining NAF in these systems...

Host-guest interactions are important to the design of pharmaceuticals and, more broadly, to soft materials as they can enable targeted, strong, and specific interactions between molecules. The binding process between the host and guest may be classified as a "rare event" when viewing the system at atomic scales, such as those explored in molecular dynamics simulations. To obtain equilibrium binding conformations and dissociation constants from these simulations, it is essential to resolve these rare events...

In response to the escalating threat of drug-resistant fungi to human health, there is an urgent need for innovative strategies. Our focus is on addressing this challenge by exploring a previously untapped target, yeast casein kinase (Yck2), as a potential space for antifungal development. To identify promising antifungal candidates, we conducted a thorough screening of the diverse-lib drug-like molecule library, comprising 99,288 molecules. Five notable drug-like compounds with diverse-lib IDs 24334243, 24342416, 17516746, 17407455, and 24360740 were selected based on their binding energy scores surpassing 11 Kcal/mol...

Cell-specific transcriptional regulatory networks (TRNs) play vital roles in plant development and response to environmental stresses. However, traditional single-cell mono-omics techniques are unable to directly capture the relationships and dynamics between different layers of molecular information within the same cells. While advanced algorithm facilitates merging scRNA-seq and scATAC-seq datasets, accurate data integration remains a challenge, particularly when investigating cell-type-specific TRNs. By examining gene expression and chromatin accessibility simultaneously in 16,670 Arabidopsis root tip nuclei, the TRNs are reconstructed that govern root tip development under osmotic stress...

BACKGROUND OBJECTIVES: Dengue fever is a mosquito-borne illness that affects millions of people worldwide every year. With no vaccination available, early detection and treatment is critical. One-hundred-twelve countries in the world pose a risk to travelers, particularly in metropolitan areas. Laboratory diagnoses vary according to objectives, resources, and schedule, with sensitivity and specificity must be balanced for effective testing. METHODS: The current work is a cross-sectional diagnostic study and samples from suspected patients of dengue was collected from May 15 to November 15 2023 and transported to laboratory, and RT-PCR and Dengue Duo Rapid test diagnosis techniques were used on 48 clinical samples included in this study...

L-cysteine is an important sulfur-containing amino acid being difficult to produce by microbial fermentation. Due to the lack of high-throughput screening methods, existing genetically engineered bacteria have been developed by simply optimizing the expression of L-cysteine-related genes one by one. To overcome this limitation, in this study, a biosensor-based approach for multilevel biosynthetic pathway optimization of L-cysteine from the DecR regulator variant of Escherichia coli was applied. Through protein engineering, we obtained the DecRN29Y/C81E/M90Q/M99E variant-based biosensor with improved specificity and an 8...

The present work focuses on the dynamics of the ionic constituents of 1-propyl-3-methyl-imidazolium-bis-(trifluormethylsulfonyl)-imide (PT), a paradigmatic ionic liquid, as an additive in poly(vinylpyrrolidone) (PVP). Hence, the resulting product can be regarded as a polymer electrolyte as well as an amorphous dispersion. Leveraging dielectric spectroscopy and oscillatory shear rheology, complemented by differential scanning calorimetry, the spectral shapes and the relaxation maps of the supercooled PVP-PT mixtures are accessed in their full compositional range...

Broadband emission in hybrid lead halide perovskites (LHPs) has gained significant attention due to its potential applications in optoelectronic devices. The origin of this broadband emission is primarily attributed to the interactions between electrons and phonons. Most investigations have focused on the impact of structural characteristics of LHPs on broadband emission, while neglecting the role of electronic mobility. In this work, the study investigates the electronic origins of broadband emission in a family of 2D LHPs...

The rise of pyrazinamide (PZA)-resistant strains of Mycobacterium tuberculosis (MTB) poses a major challenge to conventional tuberculosis (TB) treatments. PZA, a cornerstone of TB therapy, must be activated by the mycobacterial enzyme pyrazinamidase (PZase) to convert its active form, pyrazinoic acid, which targets the ribosomal protein S1. Resistance, often associated with mutations in the RpsA protein, complicates treatment and highlights a critical gap in the understanding of structural dynamics and mechanisms of resistance, particularly in the context of the G97D mutation...

This paper presents a comprehensive investigation of mesoporous Silica utilizing a multi-scale modeling approach under periodic boundary conditions integrated with machine learning algorithms. The study begins with Molecular Dynamics (MD) simulations to extract Silica's elastic properties and thermal conductivity at the nano-scale, employing the Tersoff potential. Subsequently, the derived material characteristics are applied to a series of generated porous Representative Volume Elements (RVEs) at the microscale...

Precision medicine is transforming colorectal cancer treatment through the integration of advanced technologies and biomarkers, enhancing personalized and effective disease management. Identification of key driver mutations and molecular profiling have deepened our comprehension of the genetic alterations in colorectal cancer, facilitating targeted therapy and immunotherapy selection. Biomarkers such as microsatellite instability (MSI) and DNA mismatch repair deficiency (dMMR) guide treatment decisions, opening avenues for immunotherapy...

Critical care medicine in the 21st century has witnessed remarkable advancements that have significantly improved patient outcomes in intensive care units (ICUs). This abstract provides a concise summary of the latest developments in critical care, highlighting key areas of innovation. Recent advancements in critical care include Precision Medicine: Tailoring treatments based on individual patient characteristics, genomics, and biomarkers to enhance the effectiveness of therapies. The objective is to describe the recent advancements in Critical Care Medicine...

Many enzymes display non-Arrhenius behavior with curved Arrhenius plots in the absence of denaturation. There has been significant debate about the origin of this behavior and recently the role of the activation heat capacity (Δ C P ⧧ ) has been widely discussed. If enzyme-catalyzed reactions occur with appreciable negative values of Δ C P ⧧ (arising from narrowing of the conformational space along the reaction coordinate), then curved Arrhenius plots are a consequence. To investigate these phenomena in detail, we have collected high precision temperature-rate data over a wide temperature interval for a model glycosidase enzyme MalL, and a series of mutants that change the temperature-dependence of the enzyme-catalyzed rate...

A limiting factor for solid polymer electrolyte (SPE)-based Li-batteries is the functionality of the electrolyte decomposition layer that is spontaneously formed at the Li metal anode. A deeper understanding of this layer will facilitate its improvement. This study investigates three SPEs - polyethylene oxide:lithium tetrafluoroborate (PEO:LiBF4 ), polyethylene oxide:lithium bis(oxalate)borate (PEO:LiBOB), and polyethylene oxide:lithium difluoro(oxalato)borate (PEO:LiDFOB) - using a combination of electrochemical impedance spectroscopy (EIS), galvanostatic cycling, in situ Li deposition photoelectron spectroscopy (PES), and ab initio molecular dynamics (AIMD) simulations...