Related papers: Free-energy landscape of polymer-crystal polymorph…
Monte Carlo computer simulations are used to study the segregation behaviour of two polymers under cylindrical confinement. Using a multiple-histogram method, the conformational free energy, F, of the polymers was measured as a function of…
The knowledge of the Free Energy Landscape topology is the essential key to understand many biochemical processes. The determination of the conformers of a protein and their basins of attraction takes a central role for studying molecular…
We perform a comprehensive survey of the potential energy landscapes of 13-atom Morse clusters, and describe how they can be characterized and visualized. Our aim is to detail how the global features of the funnel-like surface change with…
We analyze a recent claim that almost all closed, finite dimensional quantum systems have trap-free (i.e., free from local optima) landscapes (B. Russell et.al. J. Phys. A: Math. Theor. 50, 205302 (2017)). We point out several errors in the…
When studying high-dimensional dynamical systems such as macromolecules, quantum systems and polymers, a prime concern is the identification of the most probable states and their stationary probabilities or free energies. Often, these…
Single partially confined collapsed polymers are studied in two dimensions. They are described by self-avoiding random walks with nearest-neighbour attractions below the $\Theta$-point, on the surface of an infinitely long cylinder. For the…
We propose a biochemical model providing the kinetic and energetic descriptions of the processivity dynamics of kinesin and dinein molecular motors. Our approach is a modified version of a well known model describing kinesin dynamics and…
Assessing the synthesizability of inorganic materials is a grand challenge for accelerating their discovery using computations. Synthesis of a material is a complex process that depends not only on its thermodynamic stability with respect…
We introduce a novel scheme for the mechanistic investigation of solid-solid phase transitions, which we dub \textit{metashooting}. Combining transition path sampling molecular dynamics and metadynamics, this scheme allows for both a…
Ab initio metadynamics enables extracting free-energy landscapes having the accuracy of first principles electronic structure methods. We introduce an interface between the PLUMED code that computes free-energy landscapes and…
To extend rational materials design and discovery into the space of metastable polymorphs, rapid and reliable assessment of their lifetimes is essential. Motivated by the early work of Buerger (1951), here we investigate the routes to…
Glasses are amorphous solids whose constituent particles are caged by their neighbors and thus cannot flow. This sluggishness is often ascribed to the free energy landscape containing multiple minima (basins) separated by high barriers.…
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,…
Almost all the polymer crystals have several polymorphic modifications. Their structure and existence conditions, as well as transitions between them are not understood even in the case of the 'model' polymer polyethylene (PE). For analysis…
We develop a mathematical model for the energy landscape of polyhedral supramolecular cages recently synthesized by self-assembly [Sun et al., Science 2010]. Our model includes two essential features of the experiment: (i) geometry of the…
We apply the computational methodology of phase retrieval to the problem of folding heteropolymers. The ground state fold of the polymer is defined by the intersection of two sets in the configuration space of its constituent monomers: a…
We report Monte Carlo simulations of the melting of a single-polymer crystallite. We find that, unlike most atomic and molecular crystals, such crystallites can be heated appreciably above their melting temperature before they transform to…
Predicting crystal nucleation is among the most significant long--standing challenges in condensed matter. In the system most studied (hard sphere colloids), the comparison between experiments performed using static light scattering and…
We present a new multiphase-field theory for describing pattern formation in multi-domain and/or multi-component systems. The construction of the free energy functional and the dynamic equations is based on criteria that ensure mathematical…
We present a comprehensive analysis of the landscape for full quantum-quantum control associated with the expectation value of an arbitrary observable of one quantum system controlled by another quantum system. It is shown that such full…