Related papers: Multiple Folding Pathways of the SH3 domain
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…
Synthetic driving force molecular dynamics simulations were utilized to survey grain boundary mobility in three classes of incoherent {\Sigma}3 twin boundaries: <112>, <110>, and <111> tilt boundaries. These boundaries are faceted on low…
A small model polypeptide represented in atomic detail is folded using Monte Carlo dynamics. The polypeptide is designed to have a native conformation similar to the central part of the helix-turn-helix protein ROP. Starting from a…
With the help of lattice Monte Carlo modelling of heteropolymers, we show that the necessary condition for a protein to fold on short call is to proceed through partially folded intermediates. These elementary structures are formed at an…
The spin transition in LaCoO3 is investigated by temperature-dependent resonant soft X-ray emission spectroscopy near the Co 2p absorption edges. This element-specific technique is more bulk sensitive with respect to the temperature induced…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
Reaching a ground state of a spin system is analogous to a protein evolving into its native state. We study the ``folding'' times for various random Ising spin systems and determine characteristic temperatures that relate to the…
We model the dynamics of two species of bosonic atoms trapped in an optical lattice within the Mott regime by mapping the system onto a spin model. A field gradient breaks the cloud into two domains. We study how the domain wall evolves…
In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very…
Detecting conformational transitions in molecular systems is key to understanding biological processes. Here, we investigate the force variance in single-molecule pulling experiments as an indicator of molecular folding transitions. We…
There are some particular one-dimensional models, such as the Ising-Heisenberg spin models with a variety of chain structures, which exhibit unexpected behaviors quite similar to the first and second order phase transition, which could be…
In this work, we study the dynamics of complex systems with time-dependent transition rates, focusing on $p$-adic analysis in modeling such systems. Starting from the master equation that governs the stochastic dynamics of a system with a…
We study the thermodynamics and kinetics of folding for a small peptide. Our data rely on Monte Carlo simulations where the interactions among all atoms are taken into account. Monte Carlo kinetics is used to study folding of the peptide at…
We study QCD with massless quarks on $\mathbb{R}^3\times S^1$ under symmetry-twisted boundary conditions with small compactification radius, i.e. at high temperatures. Under suitable boundary conditions, the theory acquires a part of the…
In the framework of a lattice-model study of protein folding, we investigate the interplay between designability, thermodynamic stability, and kinetics. To be ``protein-like'', heteropolymers must be thermodynamically stable, stable against…
We investigate the phase behaviour of a two-dimensional colloidal model system of ultra-soft particles on a substrate which varies periodically along one spatial direction. Our calculations are based on mean-field density functional theory…
The dynamics of motor protein molecules that have two subunits is investigated using simple discrete stochastic models. Exact steady-state analytical expressions are obtained for velocities and dispersions for any number of intermediate…
Recent single-molecule force measurements on single-domain proteins have highlighted a three-state folding mechanism where a stabilized intermediate state (I) is observed on the folding trajectory between the stretched state and the native…
Local conduction at domains and domains walls is investigated in BiFeO3 thin films containing mostly 71o domain walls. Measurements at room temperature reveal conduction through 71o domain walls. Conduction through domains could also be…
Using holographic duality, we investigate the impact of finite temperature on the instability and splitting patterns of quadruply quantized vortices, providing the first-ever analysis in this context. Through linear stability analysis, we…