Related papers: Thermodynamically Optimized Machine-learned Reacti…
We determine the phase diagram of liquid supercooled water by extensive computer simulations using the TIP5P-E model [J. Chem. Phys. {\bf 120}, 6085 (2004)]. We find that the transformation of water into a low density liquid in the…
We present two methods to reveal protein-ligand unbinding mechanisms in biased unbinding simulations by clustering trajectories into ensembles representing unbinding paths. The first approach is based on a contact principal component…
Nonintegrability plays a crucial role in thermalization and transport processes in many-body Hamiltonian systems, yet its quantitative effects remain unclear. To reveal the connection between the macroscopic relaxation properties and the…
The hydrophobic effect stabilizes the native structure of proteins by minimizing the unfavourable interactions between hydrophobic residues and water through the formation of a hydrophobic core. Here we include the entropic and enthalpic…
This thesis investigates the interactions of different degrees of freedom of one joint system within the theory of stochastic thermodynamics. First, a comprehensive introduction to the subjects of stochastic processes, information theory…
In equilibrium and supercooled liquids, polymorphism is manifested by thermodynamic regions defined in the phase diagram, which are predominantly of different short- and medium-range order (local structure). It is found that on the phase…
Based on our recent study on physical origin of hydrophobic effects, this is applied to investigate the dependence of hydrophobic interactions on the solute size. As two same hydrophobic solutes are dissolved into water, the hydration free…
Colloidal aggregation could be implemented in various fields ranging from purely colloidal thermodynamics to protein interactions, their stability, and maybe folding. Indeed, colloidal aggregation is closely linked to the so-called…
A rigorous formalism for estimating noncovalent binding free energies and thermodynamic expectations from calculations in which receptor configurations are sampled independently from the ligand is derived. Due to this separation, receptor…
Complex natural or engineered systems comprise multiple characteristic scales, multiple spatiotemporal domains, and even multiple physical closure laws. To address such challenges, we introduce an interface learning paradigm and put forth a…
Water is vital for life, and without it biomolecules and cells cannot maintain their structures and functions. The remarkable properties of water originate from its ability to form hydrogen-bonding networks and dynamics, which the…
The interface between liquid water and the Pt(111) metal surface is characterized structurally and thermodynamically via reactive molecular dynamics (MD) simulations within the ReaxFF framework. The formation of a distinct buckled adsorbate…
Prediction of protein-ligand binding affinity is a major goal in drug discovery. Generally, free energy gap is calculated between two states (e.g., ligand binding and unbinding). The energy gap implicitly includes the effects of changes in…
In physical networks trained using supervised learning, physical parameters are adjusted to produce desired responses to inputs. An example is electrical contrastive local learning networks of nodes connected by edges that are resistors…
A comprehensive, semi-quantitative model for the thermodynamics of hydrophobic solvation is presented. The model is based on a very simple premise suggested by the scaled particle theory and treats both solute and solvent molecules as hard…
Searching for reaction pathways describing rare events in large systems presents a long-standing challenge in chemistry and physics. Incorrectly computed reaction pathways result in the degeneracy of microscopic configurations and inability…
Protein-ligand interactions are crucial for a wide range of physiological processes. Many cellular functions result in these non-covalent `bonds' being mechanically strained, and this can be integral to proper cellular function. Broadly,…
The process of ligand-protein unbinding is crucial in biophysics. Water is an essential part of any biological system and yet, many aspects of its role remain elusive. Here, we simulate with state-of-the-art enhanced sampling techniques the…
The hydrophobic interaction, often combined with the hydrophilic or ionic interactions, makes the behavior of aqueous solutions very rich and plays an important role in biological systems. Theoretical and computer simulation studies haven…
Hydrogen bonding is modeled in terms of virtual exchange of protons between water molecules. A simple lattice model is analyzed, using ideas and techniques from the theory of correlated electrons in metals. Reasonable parameters reproduce…