Molecular dynamics simulations of protein folding and unfolding are often carried out at temperatures (400-600 K) that are much higher than physiological or room temperature to speed up the (un)folding process. Use of such high temperatures changes both the protein and solvent properties considerably, compared to physiological or room temperature. Water models designed for use in conjunction wi...

Over the past three decades the protein folding field has undergone monumental changes. Originally a purely academic question, how a protein folds has now become vital in understanding diseases and our abilities to rationally manipulate cellular life by engineering protein folding pathways. We review and contrast past and recent developments in the protein folding field. Specifically, we discus...

β-Sheet mediated protein-protein interactions are involved in key signalling pathways in diseases such as cancer. We present small molecule β-strand mimetics and investigate their interactions with a model tripeptide. Using (1)H NMR, the thermodynamic parameters for their binding are determined. These give insight into this biologically important interaction.

We propose a thermodynamics-based learning strategy for non-equilibrium evolution equations based on Onsager's variational principle, which allows to write such PDEs in terms of two potentials: the free energy and dissipation potential. Specifically, these potentials are learned from spatio-temporal measurements macroscopic observables via proposed neural network architectures that strongly enf...

The birth, raise, development and fortunes of a fundamental theory in thermodynamics, the axiomatic thermodynamics, a creation of Constantin Carathéodory, is thoroughly presented together with a summary of Carathéodory’s biography. Axiomatic thermodynamics is centered around some interesting properties of Pfaffian differential equations, which are here introduced and used for some well-known ca...

isotherm equation is one of the important scientific bases for adsorbent selection. there are different isotherms that do not account for an adsorbate, different chemisorption geometries on the nanoporous surface. it is interesting to introduce a general isotherm, which considers different chemisorption geometries of an adsorbate on nanoporous surfaces. in this study, an isotherm for non-dissoci...

Small DNA circles can occur in Nature, for example as protein-constrained loops, and can be synthesized by a number of methods. Such small circles provide tractable systems for the study of the structure, thermodynamics and molecular dynamics of closed-circular DNA. In the present article, we review the occurrence and synthesis of small DNA circles, and examine their utility in studying the pro...

Entanglement entropy is often speculated as a strong candidate for the origin of the black-hole entropy. To judge whether this speculation is true or not, it is effective to investigate the whole structure of thermodynamics obtained from the entanglement entropy, rather than just to examine the apparent structure of the entropy alone or to compare it with that of the black hole entropy. It is b...

Recently, protein-folding models have advanced to the point where folding simulations of protein-like chains of reasonable length (up to 125 amino acids) are feasible, and the major physical features of folding proteins, such as cooperativity in thermodynamics and nucleation mechanisms in kinetics, can be reproduced. This has allowed deep insight into the physical mechanism of folding, includin...

By perturbing a G(o) model toward a realistic protein Hamiltonian by adding non-native interactions, we find that the folding rate is in general enhanced as ruggedness is initially increased, as long as the protein is sufficiently large and flexible. Eventually, the rate drops rapidly toward zero when ruggedness significantly slows conformational transitions. Energy landscape arguments for ther...