Related papers: Exploring the Thermostability of CRISPR Cas12b usi…

We model the well-known interlinked cascade of Rab GTPases found in eukaryotic cells by using a network of Markov states to investigate the universal Thermodynamic Uncertainty Relation for the non-equilibrium system. First, we prove…

Crystallization is one of the most important physicochemical processes which has relevance in material science, biology, and the environment. Decades of experimental and theoretical efforts have been made to understand this fundamental…

In this work we study, at the single molecular level, the thermodynamic and dynamic characteristics of an enzymatic reaction comprising a rate limiting step. We investigate how the stability of the enzyme-state stationary probability…

Multiple time scale molecular dynamics enhances computational efficiency by updating slow motions less frequently than fast motions. However, in practice the largest outer time step possible is limited not by the physical forces but by…

Background: Current research suggests that a small set of "driver" mutations are responsible for tumorigenesis while a larger body of "passenger" mutations occurs in the tumor but does not progress the disease. Due to recent pharmacological…

We report a velocity selective bi-polarization spectroscopy (VS-BPS) technique to generate a background-free, dispersion-like reference signal which is tunable over a wide range of frequency. In this technique, a pair of linearly polarized…

Matching promises transparent causal inferences for observational data, making it an intuitive approach for many applications. In practice, however, standard matching methods often perform poorly compared to modern approaches such as…

This work expands on our recently introduced low Mach enthalpy method [1] for simulating the melting and solidification of a phase change material (PCM) alongside (or without) an ambient gas phase. The method captures PCM's volume change…

Unraveling the dynamical motions of biomolecules is essential for bridging their structure and function, yet it remains a major computational challenge. Molecular dynamics (MD) simulation provides a detailed depiction of biomolecular…

Protein folding is an indispensable process for the majority of proteins after their synthesis from ribosomes in the cell. Most in vitro protein folding studies have focused on single-domain proteins. Hence, it is important to understand…

In molecular dynamics (MD) simulations, accessing transition probabilities between states is crucial for understanding kinetic information, such as reaction paths and rates. However, standard MD simulations are hindered by the capacity to…

Availability of high-resolution crystal structures of ribosomal subunits of different species opens a route to investigate about molecular interactions between its constituents and stabilization strategy. Structural analysis of the small…

We present a comprehensive characterization of cold molecular beams from a cryogenic buffer-gas cell, providing an insight into the physics of buffer-gas cooling. Cold molecular beams are extracted from a cryogenic cell by electrostatic…

In this work structural refinement, complex impedance spectroscopy, and Raman spectroscopy have been investigated on Na$_{0.5}$(Bi$_{1-x}$Dy$_x$)$_{0.5}$TiO$_3$ (xDyNBT) ceramic systems. The pure NBT, 2DyNBT and 5DyNBT compounds crystallize…

The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…

Using the perturbation-response scanning (PRS) technique, we study a set of 23 proteins that display a variety of conformational motions upon ligand binding (e.g. shear, hinge, allosteric). In most cases, PRS determines residues that may be…

Using a coarse molecular-dynamics (CMD) approach with an appropriate choice of coarse variable (order parameter), we map the underlying effective free-energy landscape for the melting of a crystalline solid. Implementation of this approach…

In recent years, orientationally disordered crystals, or plastic crystals, have transformed the field of solid-state cooling due to the significant latent heat and entropy changes associated with their temperature induced molecular…

Despite the significant increase in computational power, molecular modeling of protein structure using classical all-atom approaches remains inefficient, at least for most of the protein targets in the focus of biomedical research. Perhaps…

We review the background, theory and general equations for the analysis of equilibrium protein unfolding experiments, focusing on denaturant and heat-induced unfolding. The primary focus is on the thermodynamics of reversible…