Related papers: New method for deciphering free energy landscape o…
Motivated by solid-solid phase transitions in elastic thin films, we perform a Gamma-convergence analysis for a singularly perturbed energy describing second order phase transitions in a domain of vanishing thickness. Under a two-wells…
The interconversion between left- and right-handed helical folds of a polypeptide defines a dual-funneled free energy landscape. In this context, the funnel minima are connected through a continuum of unfolded conformations, evocative of…
An analysis of the network defined by the potential energy minima of multi-atomic systems and their connectivity via reaction pathways that go through transition states allows to understand important characteristics like thermodynamic,…
Reinforcement learning (RL) has shown its strength in challenging sequential decision-making problems. The reward function in RL is crucial to the learning performance, as it serves as a measure of the task completion degree. In real-world…
Recent experimental results suggest that the native fold, or topology, plays a primary role in determining the structure of the transition state ensemble, at least for small fast folding proteins. To investigate the extent of the…
We extend the non-parametric framework of reaction coordinate optimization to non-equilibrium ensembles of (short) trajectories. For example, we show how, starting from such an ensemble, one can obtain an equilibrium free energy profile…
We investigate relaxation dynamics along the entire first-order phase transition line by analyzing the time evolution of the free energy landscape in the three-dimensional kinetic Ising model. Near the critical temperature $T_{\rm c}$, the…
The assembly of proteins in membranes plays a key role in many crucial cellular pathways. Despite their importance, characterizing transmembrane assembly remains challenging for experiments and simulations. Equilibrium molecular dynamics…
We consider two- and three-dimensional lattice models of proteins which were characterized previously. We coarse grain their folding dynamics by reducing it to transitions between effective states. We consider two methods of selection of…
We investigate the kinetics and the free energy landscape of the crystallization of hard spheres from a supersaturated metastable liquid though direct simulations and forward flux sampling. In this first paper, we describe and test two…
In this work, we present a phase-field model for tumour growth, where a diffuse interface separates a tumour from the surrounding host tissue. In our model, we consider transport processes by an internal, non-solenoidal velocity field. We…
The minimal time required for a system to evolve between two different states is an important notion for developing ultra-speed quantum computer and communication channel. Here, we introduce a new metric for non-degenerate density operator…
Activated processes from chemical reactions up to conformational transitions of large biomolecules are hampered by barriers which are overcome only by the input of some free energy of activation. Hence, the characteristic and…
Describing the complex landscape of infinite-dimensional free energy is generally a challenging problem. This difficulty arises from the existence of numerous minimizers and, consequently, a vast number of saddle points. These factors make…
Identification of critical residues of a protein is actively pursued, since such residues are essential for protein function. We present three ways of recognising critical residues of an example protein, the evolution of which is tracked…
Deep reinforcement learning (DRL) has been shown to achieve high performance on locomotion control tasks in MuJoCo benchmarks such as HalfCheetah, Ant, and Walker2D. However, visualizing the motion structures internally obtained by a…
Learning a Markov Decision Process (MDP) from a fixed batch of trajectories is a non-trivial task whose outcome's quality depends on both the amount and the diversity of the sampled regions of the state-action space. Yet, many MDPs are…
We consider two types of Go models of a protein (crambin) and study their kinetics through molecular dynamics simulations. In the first model, the residue -- residue contact interactions are selected based on a cutoff distance, $R_c$,…
An energy gap develops near quantum critical point of quantum phase transition in a finite many-body (MB) system, facilitating the ground state transformation by adiabatic parameter change. In real application scenarios, however, the…
A stochastic process, when subject to resetting to its initial condition at a constant rate, generically reaches a non-equilibrium steady state. We study analytically how the steady state is approached in time and find an unusual relaxation…