Omar Valsson

Omar Valsson
University of North Texas | UNT · Department of Chemistry

PhD

About

37
Publications
3,494
Reads
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1,452
Citations
Additional affiliations
April 2017 - present
Max Planck Institute for Polymer Research
Position
  • Project Manager
October 2012 - March 2017
USI Lugano
Position
  • PhD Student
October 2012 - March 2017
ETH Zurich
Position
  • PhD Student
Education
September 2008 - September 2012
University of Twente
Field of study
  • Physics
September 2006 - June 2008
University of Iceland
Field of study
  • Physics
September 2003 - June 2006
University of Iceland
Field of study
  • Physics

Publications

Publications (37)
Preprint
Full-text available
The expansive production of data in materials science, their widespread sharing and repurposing requires educated support and stewardship. In order to ensure that this need helps rather than hinders scientific work, the implementation of the FAIR-data principles (Findable, Accessible, Interoperable, and Reusable) must not be too narrow. Besides, th...
Preprint
Collective variable-based enhanced sampling methods are routinely used on systems with metastable states, where high free energy barriers impede proper sampling of the free energy landscapes when using conventional molecular dynamics simulations. One such method is variationally enhanced sampling (VES), which is based on a variational principle whe...
Preprint
Full-text available
Enhanced sampling algorithms have emerged as powerful methods to extend the potential of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems. This review aims to present the unifying principles and differences of several computational methods for enhanced sampling in molecular simul...
Article
Full-text available
Most of the artwork and cultural heritage objects are stored in museums under conditions that are difficult to monitor. While advanced technologies aim to control and prevent the degradation of cultural heritage objects in line with preventive conservation measures, there is much to be learned in terms of the physical processes that lead to the deg...
Article
Full-text available
Machine learning methods provide a general framework for automatically finding and representing the essential characteristics of simulation data. This task is particularly crucial in enhanced sampling simulations. There we seek a few generalized degrees of freedom, referred to as collective variables (CVs), to represent and drive the sampling of th...
Article
Full-text available
Polymorphism rationalizes how processing can control the final structure of a material. The rugged free-energy landscape and exceedingly slow kinetics in the solid state have so far hampered computational investigations. We report for the first time the free-energy landscape of a polymorphic crystalline polymer, syndiotactic polystyrene. Coarse-gra...
Article
RNA molecules selectively bind to specific metal ions to populate their functional active states making it important to understand their source of ion selectivity. In large RNA systems, metal ions interact with the RNA at multiple locations making it difficult to decipher the precise role of ions in folding. To overcome this complexity, we studied...
Preprint
Full-text available
Polymorphism rationalizes how processing can control the final structure of a material. The rugged free-energy landscape and exceedingly slow kinetics in the solid state have so far hampered computational investigations. We report for the first time the free-energy landscape of a polymorphic crystalline polymer, syndiotactic polystyrene. Coarse-gra...
Preprint
Full-text available
Machine learning methods provide a general framework for automatically finding and representing the essential characteristics of simulation data. This task is particularly crucial in enhanced sampling simulations, where we seek a few generalized degrees of freedom, referred to as collective variables (CVs), to represent and drive the sampling of th...
Preprint
Full-text available
RNA molecules selectively bind to specific metal ions to populate their functional active states making it important to understand their source of ion selectivity. In large RNA systems, metal ions interact with the RNA at multiple locations making it difficult to decipher the precise role of ions in folding. To overcome this complexity, we studied...
Article
Full-text available
Searching for reaction pathways describing rare events in large systems presents a long-standing challenge in chemistry and physics. Incorrectly computed reaction pathways result in the degeneracy of microscopic configurations and inability to sample hidden energy barriers. To this aim, we present a general enhanced sampling method to find multiple...
Preprint
Full-text available
Searching for reaction pathways of large systems presents a long-standing challenge in physics. We present a general molecular dynamics method to find multiple diverse reaction pathways of ligand unbinding through minimization of a loss function describing ligand--protein interactions. The method successfully overcomes large energy barriers using a...
Article
Full-text available
The numerical computation of chemical potential in dense, non-homogeneous fluids is a key problem in the study of confined fluids thermodynamics. To this day several methods have been proposed, however there is still need for a robust technique, capable of obtaining accurate estimates at large average densities. A widely established technique is th...
Article
Full-text available
The ability to predict accurate thermodynamic and kinetic properties in biomolecular systems is of both scientific and practical utility. While both remain very difficult, predictions of kinetics are particularly difficult because rates, in contrast to free energies, depend on the route taken and are thus not amenable to all enhanced sampling metho...
Article
Many enhanced sampling methods, such as Umbrella Sampling, Metadynamics or Variationally Enhanced Sampling, rely on the identification of appropriate collective variables. For proteins, even small ones, finding appropriate collective variables has proven challenging. Here we suggest that the NMR $S^2$ order parameter can be used to this effect. We...
Article
A powerful way to deal with a complex system is to build a coarse-grained model capable of catching its main physical features, while being computationally affordable. Inevitably, such coarse-grained models introduce a set of phenomenological parameters, which are often not easily deducible from the underlying atomistic system. We present a unique...
Article
We have studied the reaction dynamics of a prototypical organic reaction using a variationally optimized truncated bias to accelerate transitions between educts and products reactant states. The asymmetric SN2nucleophilic substitution reaction of fluoromethane and chloromethane CH3F + Cl- <=> CH3Cl + F- is considered and many independent biased mol...
Article
Crystallization is a process of great practical relevance in which rare but crucial fluctuations lead to the formation of a solid phase starting from the liquid. Like in all first order first transitions there is an interplay between enthalpy and entropy. Based on this idea, we introduce two collective variables, one enthalpic and the other entropi...
Article
In recent work, we demonstrated that it is possible to obtain approximate representations of high-dimensional free energy surfaces with variationally enhanced sampling (Shaffer, P.; Valsson, O.; Parrinello, M. Proc. Natl. Acad. Sci.,2016, 113, 17). The high-dimensional spaces considered in that work were the set of backbone dihedral angles of a sma...
Article
Full-text available
Light-sensing in photoreceptor proteins is subtly modulated by the multiple interactions between the chromophoric unit and its binding pocket. Many theoretical and experimental studies have tried to uncover the fundamental origin of these interactions but reached contradictory conclusions as to whether electrostatics, polarization, or intrinsically...
Article
We study by computer simulation the nucleation of a supersaturated Lennard-Jones vapor into the liquid phase. The large free energy barriers to transition make the time scale of this process impossible to study by ordinary molecular dynamics simulations. Therefore we use a recently developed enhanced sampling method [Valsson and Parrinello, Phys. R...
Article
Atomistic simulations play a central role in many fields of science. However, their usefulness is often limited by the fact that many systems are characterized by several metastable states separated by high barriers, leading to kinetic bottlenecks. Transitions between metastable states are thus rare events that occur on significantly longer timesca...
Article
Obtaining efficient sampling of multiple metastable states through molecular dynamics and hence determining free energy differences is central for understanding many important phenomena. Here we present a new biasing strategy, which employs the recent variationally enhanced sampling approach (Valsson and Parrinello, Phys. Rev. Lett. 2014, 113, 0906...
Article
The capabilities of molecular simulations have been greatly extended by a number of widely used enhanced sampling methods that facilitate escaping from metastable states and crossing large barriers. Despite these developments there are still many problems which remain out of reach for these methods which has led to a vigorous effort in this area. O...
Article
Full-text available
We propose a new method to obtain kinetic properties of infrequent events from molecular dynamics simulation. The procedure employs a recently introduced variational approach [Valsson and Parrinello, Phys. Rev. Lett. 113, 090601 (2014)] to construct a bias potential which acts in the space spanned by a small number of collective variables and is de...
Article
We propose a simple yet effective iterative scheme that allows us to employ the well-tempered distribution as a target distribution for the collective variables in our recently introduced variational approach to enhanced sampling and free energy calculations [Valsson and Parrinello, Phys. Rev. Lett. 2014, 113, 090601]. The performance of the scheme...
Article
Full-text available
The excited-state relaxation of retinal protonated Schiff bases (PSBs) is an important test case for biological applications of time-dependent (TD) density-functional theory (DFT). While well-known shortcomings of approximate TD-DFT might seem discouraging for application to PSB relaxation, progress continues to be made in the development of new fu...
Article
The ability of widely used sampling methods, such as molecular dynamics or Monte Carlo, to explore complex free energy landscapes is severely hampered by the presence of kinetic bottlenecks. A large number of solutions have been proposed to alleviate this problem. Many are based on the introduction of a bias potential which is a function of a small...
Article
We explore the performance of the well-tempered ensemble combined with parallel tempering (PT-WTE) in obtaining a thermodynamical description of a given molecular system. We carefully explain the theoretical procedure employed to extract all the relevant thermodynamical quantities from a PT-WTE simulation. As a specific molecular system, we conside...
Article
Embedding potentials are frequently used to describe the effect of an environment on the electronic structure of molecules in larger systems, including their excited states. If such excitations are accompanied by significant rearrangements in the electron density of the embedded molecule, large differential polarization effects may take place, whic...
Article
Bovine rhodopsin is the most extensively studied retinal protein and is considered the prototype of this important class of photosensitive biosystems involved in the process of vision. Many theoretical investigations have attempted to elucidate the role of the protein matrix in modulating the absorption of retinal chromophore in rhodopsin, but, whi...
Article
We employ a variety of highly-correlated approaches including quantum Monte Carlo (QMC) and the n-electron valence state perturbation theory (NEVPT2) to compute the vertical excitation energies of retinal protonated Schiff base (RPSB) models in the gas phase. We find that the NEVPT2 excitation energies are in good agreement with the QMC values and...
Article
We employ state-of-the-art first-principle approaches to investigate whether temperature effects are responsible for the unusually broad and flat spectrum of protonated Schiff base retinal observed in photodissociation spectroscopy, as has recently been proposed. We first carefully calibrate how to construct a realistic geometrical model of retinal...
Article
The simplest cyanine dye series [H2N(CH)nNH2]+ with n = 1, 3, 5, 7, and 9 appears to be a challenge for all theoretical excited-state methods since the experimental spectra are difficult to predict and the observed deviations cannot be easily explained with standard arguments. We compute here the lowest vertical excitation energies of these dyes us...
Article
We present a systematic investigation of the structural relaxation in the excited state of model retinal chromophores in the gas phase using the complete-active-space self-consistent theory (CASSCF), multiconfigurational second-order perturbation theory (CASPT2), quantum Monte Carlo (QMC), and coupled cluster (CC) methods. In contrast to the CASSCF...
Article
We investigate phase coherent electronic transport in an open quantum system, which consists of quantum dots side-coupled to a nanowire. It is demonstrated that coherent switching can be characterized by adjusting the electronic energy. A comparative analysis of quantum coherence effects in side-coupled quantum-dot systems is presented. Our results...

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