Related papers: Energy Landscapes for Digital Alchemy
We present a novel method, which we call dual minima hopping method (DMHM), that allows us to find the global minimum of the potential energy surface (PES) within density functional theory for systems where a fast but less accurate…
Protein folding processes are generally described statistically with the help of multidimensional free energy landscape, typically reduced to a 1-D free energy profile along good reaction co-ordinate. There are many physical parameters…
Recently a non-empirical stochastic walker algorithm has been developed to search for the minimum-energy escape paths (MEP) from the minima of the potential surface [J. Phys. Soc. Jpn. 87, 063801 (2018); Physica A, 528, 121481 (2019)]. This…
Gene expression profiles are essential in identifying different cancer phenotypes. Clustering gene expression datasets can provide accurate identification of cancerous cell lines, but this task is challenging due to the small sample size…
A parameter method is introduced in order to estimate the relationship among the various variables of a system in equilibrium, where the potential energy functions are incompletely known or the quantum mechanical calculations very…
Quantum algorithms for ground-state energy estimation of chemical systems require a high-quality initial state. However, initial state preparation is commonly either neglected entirely, or assumed to be solved by a simple product state like…
Translating the complex, multi-dimensional data from simulations of biomolecules to intuitive knowledge is a major challenge in computational chemistry and biology. The so-called "free energy landscape" is amongst the most fundamental…
The aim of this work is to study the physical properties of a one-way quantum computer in an effective low-energy cluster state. We calculate the optimal working conditions as a function of the temperature and of the system parameters. The…
With the help of a simple 20 letters, lattice model of heteropolymers, we investigate the energy landscape in the space of designed good-folder sequences. Low-energy sequences form clusters, interconnected via neutral networks, in the space…
The chemical dynamics scene is the most important application of computer simulation. We show that electrons jump between potential holes of different depths (new molecular orbits, hybrid atomic orbits with different energies) under the…
Performing alchemical transformations, in which one molecular system is nonphysically changed to another system, is a popular approach adopted in performing free energy calculations associated with various biophysical processes, such as…
This article is devoted to the study of certain models for phase transitions involving nonlocal energies. A first part is concerned with to the asymptotic analysis of a system of fractional elliptic equations of Allen-Cahn type as a…
A central concern of molecular dynamics simulations are the potential energy surfaces that govern atomic interactions. These hypersurfaces define the potential energy of the system, and have generally been calculated using either predefined…
We view Digital Ecosystems to be the digital counterparts of biological ecosystems. Here, we are concerned with the creation of these Digital Ecosystems, exploiting the self-organising properties of biological ecosystems to evolve…
We describe a robust and efficient chain-of-states method for computing Minimum Energy Paths~(MEPs) associated to barrier-crossing events in poly-atomic systems. The path is parametrized in terms of a continuous variable $t \in [0,1]$ that…
Landau's theory of phase transitions is adapted to treat independently relaxing regions in complex systems using nanothermodynamics. The order parameter we use governs the thermal fluctuations, not a specific static structure. We find that…
An equilibrated model glass-forming liquid is studied by mapping successive configurations produced by molecular dynamics simulation onto a time series of inherent structures (local minima in the potential energy). Using this ``inherent…
Based on an analysis of the short range chemical environment of each atom in a system, standard machine learning based approaches to the construction of interatomic potentials aim at determining directly the central quantity which is the…
We present an efficient method to find minimum energy structures using energy estimates from accurate quantum Monte Carlo calculations. This method involves a stochastic process formed from the stochastic energy estimates from Monte Carlo…
A method is presented that can find the global minimum of very complex condensed matter systems. It is based on the simple principle of exploring the configurational space as fast as possible and of avoiding revisiting known parts of this…