Related papers: pH modulates friction memory effects in protein fo…
The influence of the salts KCl, NaCl, and NaI at molar concentrations on the {\alpha}-helical folding kinetics of the alanine-based oligopeptide Ace-AEAAAKEAAAKA-Nme is investigated by means of (explicit-water) molecular dynamics…
Battery degradation is governed by complex and randomized cyclic conditions, yet existing modeling and prediction frameworks usually rely on rigid, unchanging protocols that fail to capture real-world dynamics. The stochastic electrical…
Generative diffusion models have emerged as powerful tools for sampling high-dimensional distributions, yet they typically rely on white gaussian noise and noise schedules to destroy and reconstruct information. Here, we demonstrate that…
We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…
We investigate the thermodynamics of overdamped systems weakly driven by time-dependent protocols while interacting with viscoelastic heat baths. Using a generalized Langevin equation with memory, we derive the conditions under which the…
We study the kinetics of assembly of two plates of varying hydrophobicity, including cases where drying occurs and water strongly solvates the plate surfaces. The potential of mean force and molecular-scale hydrodynamics are computed from…
We consider the effects of memory on the stationary behavior of a two-dimensional Langevin dynamics in a confining potential. The system is treated in an overdamped approximation and the degrees of freedom are under the influence of…
We discuss the two-dimensional motion of a Brownian particle that is confined to a harmonic trap and driven by a shear flow. The surrounding medium induces memory effects modelled by a linear, typically nonreciprocal coupling of the…
Acid-base equilibria directly influence the functionality and behavior of particles in a system. Due to the ionizing effects of acid-base functional groups, particles will undergo charge exchange. The degree of ionization and their…
Experiments in bulk water confirm the existence of two local arrangements of water molecules with different densities, but, because of inevitable freezing at low temperature $T$, can not ascertain whether the two arrangements separate in…
Analysis of non-Markovian systems and memory induced phenomena poses an everlasting challenge for physics. As a paradigmatic example we consider a classical Brownian particle of mass $M$ subjected to an external force and exposed to…
Inverse protein folding, the process of designing sequences that fold into a specific 3D structure, is crucial in bio-engineering and drug discovery. Traditional methods rely on experimentally resolved structures, but these cover only a…
The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…
Transformer-based architectures have recently propelled advances in sequence modeling across domains, but their application to the hydrophobic-hydrophilic (H-P) model for protein folding remains relatively unexplored. In this work, we adapt…
We study the dynamics of a quantum system whose interaction with an environment is described by a collision model, i.e. the open dynamics is modelled through sequences of unitary interactions between the system and the individual…
The molecular dynamics (MD) simulation study of solvation structure and free energetics in 1-ethyl-3-methylimidazolium chloride and 1-ethyl-3-methylimidazolium hexafluorophosphate using a probe solute in the preceding article [Y. Shim, M.…
We present a novel statistical mechanics formalism for the theoretical description of the process of protein folding$\leftrightarrow$unfolding transition in water environment. The formalism is based on the construction of the partition…
Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…
We investigate the nature of memory effects in the non-Markovian dynamics of spin boson models. Local quantum memory criteria can be used to indicate that the reduced dynamics of an open system necessarily requires a quantum memory in its…
Recently there has been an intense effort to understand measurement induced transitions, but we still lack a good understanding of non-Markovian effects on these phenomena. To that end, we consider two coupled chains of free fermions, one…