Related papers: Golf-course and funnel energy landscapes: Protein …
Entropy barriers and ageing states appear in martensitic structural-transition models, slowly re-equilibrating after temperature quenches, under Monte Carlo dynamics. Concepts from protein folding and ageing harmonic oscillators turn out to…
Energetic correlations due to polymeric constraints and the locality of interactions, in conjunction with the apriori specification of the existence of a particularly low energy state, provides a method of introducing the aspect of minimal…
We present systematic temperature-quench Monte Carlo simulations on discrete-strain pseudospin model Hamiltonians to study microstructural evolutions in 2D ferroelastic transitions with two-component vector order parameters ($N_{OP}=2$).…
A three-dimensional phase-field model is proposed for simulating the magnetic martensitic phase transformation. The model considers a paramagnetic cubic austenite to ferromagnetic tetragonal martensite transition, as it occurs in magnetic…
The energy landscapes of proteins have evolved to be different from most random heteropolymers. Many studies have concluded that evolutionary selection for rapid and reliable folding to a given structure that is stable at biological…
We study the geometric properties of the energy landscape of coarse-grained, off-lattice models of polymers by endowing the configuration space with a suitable metric, depending on the potential energy function, such that the dynamical…
The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…
We use a free energy functional theory to elucidate general properties of heterogeneously ordering, fast folding proteins, and we test our conclusions with lattice simulations. We find that both structural and energetic heterogeneity can…
To test a Partial Equilibration Scenario (PES) of Ritort and colleagues, we do Monte Carlo simulations of discretized-strain spin models, for four 3D martensitic structural transitions under quenches to a bath temperature $T <T_0$ below a…
Protein folding is analyzed using a replica variational formalism to investigate some free energy landscape characteristics relevant for dynamics. A random contact interaction model that satisfies the minimum frustration principle is used…
Branching can be observed at the austenite-martensite interface of martensitic phase transformations. For a model problem, Kohn and M\"uller studied a branching pattern with optimal scaling of the energy with respect to its parameters.…
Martensites are metastable phases, possessing a characteristic morphology, usually formed during a fast quench accross a structural transition. We attempt to understand these morphological features using a coarsegrained free energy…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
We explore the possibilities and limitations of using a coherent second phase to engineer the thermo-mechanical properties of a martensitic alloy by modifying the underlying free energy landscape that controls the transformation. We use…
We do Monte Carlo simulations of four 3D structural transitions, with vector-spin models of their martensitic strain domains under quenches to $T$, to test a generic post-quench Partial Equilibration Scenario (PES) of Ritort. We indeed…
Single molecule mechanical unfolding experiments are beginning to provide profiles of the complex energy landscape of biomolecules. In order to obtain reliable estimates of the energy landscape characteristics it is necessary to combine the…
In order to better understand the occurrence of phase transitions, we adopt an approach based on the study of energy landscapes: The relation between stationary points of the potential energy landscape of a classical many-particle system…
In this study, we demonstrate how the incorporation of appropriate feature engineering together with the selection of a Machine Learning (ML) algorithm that best suits the available dataset, leads to the development of a predictive model…
An original thermodynamically consistent large strains-based multiphase phase-field (PF) approach of Ginzburg-Landau type is developed for studying the grain boundary (GB)-induced martensitic transformations (MTs) in polycrystalline…
Understanding how proteins fold into their native structure is a fundamental problem in biophysics, crucial for protein design. It has been hypothesized that the formation of a molten globule intermediate precedes folding to the native…