相关论文: Reaction Coordinates for Conformational Transition…
We consider a general class of autocatalytic reactions, that has been shown to display stochastically switching behaviour (Discreteness Induced Transitions) in some parameter regimes. This behaviour was shown to occur when either the…
The massive successes of large language models (LLMs) encourage the emerging exploration of LLM-augmented Autonomous Agents (LAAs). An LAA is able to generate actions with its core LLM and interact with environments, which facilitates the…
Structural transition induced by a local conformational change in biomolecules is formulated based on the generalized Langevin theory for the structural fluctuation of a molecule in solution, and the linear response theory, derived by Kim…
Accurate identification of late-life depression (LLD) using structural brain MRI is essential for monitoring disease progression and facilitating timely intervention. However, existing learning-based approaches for LLD detection are often…
The pattern of radiation energy deposition in substances at the microscopic level of lattice, molecule size, or the cell's nucleus is not uniform. The energy of radiation is transferred to the substance medium in the form of discrete,…
The article presents results of discrete thermodynamics (DTD) basic application to electrochemical systems. Consistent treatment of the electrochemical system as comprising two interacting subsystems - the chemical and the electrical…
Establishing correspondences is a fundamental task in variety of image processing and computer vision applications. In particular, finding the correspondences between a non-linearly deformed image pair induced by different modality…
The similarity in the three-dimensional structures of homologous proteins imposes strong constraints on their sequence variability. It has long been suggested that the resulting correlations among amino acid compositions at different…
The work is presented, leading to the universal contact molecular mechanism of phase transitions and other reactions in solid state. The two components of the mechanism - nucleation and interface propagation - are investigated in detail and…
The properties of molecule-optical elements such as lenses or prisms based on the interaction of molecules with optical fields depend in a crucial way on the molecular quantum state and its alignment created by the optical field. However,…
Living organisms maintain stable functioning amid environmental fluctuations through homeostasis, a property that preserves a system's behavior despite changes in environmental conditions. To elucidate homeostasis in stochastic biochemical…
Large language models applied to vast biological datasets have the potential to transform biology by uncovering disease mechanisms and accelerating drug development. However, current models are often siloed, trained separately on…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
This paper is devoted to the development of a theoretical and computational framework to efficiently sample the statistically significant thermally activated reaction pathways, in multi-dimensional systems obeying Langevin dynamics. We show…
Transition state or minimum energy path finding methods constitute a routine component of the computational chemistry toolkit. Standard analysis involves trajectories conventionally plotted in terms of the relative energy to the initial…
Recent theoretical studies have explored how ultra-strong light--matter coupling can be used as a handle to control chemical transformations. {\em Ab initio} cavity quantum electrodynamics (QED) calculations demonstrate that large changes…
Metabolic networks, formed by a series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell, and by a set of interactions that guide and regulate the activity of…
The role of response operators is well established in quantum mechanics. We investigate their use for universal quantum machine learning models of response properties in molecules. After introducing a theoretical basis, we present and…
We determine the evolving segregated or mixed morphology of charged-particle systems with long-range power-law interactions and overall charge neutrality that have been quenched to a low temperature. Segregated morphology systems are…
The reaction-diffusion master equation (RDME) is commonly used to model processes where both the spatial and stochastic nature of chemical reactions need to be considered. We show that the RDME in many cases is inconsistent with a…