Tomaz Urbic

Tomaz Urbic
University of Ljubljana · Department of Chemistry and Biochemistry

PhD chemistry

About

93
Publications
11,867
Reads
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967
Citations
Introduction
three partice forces, protein folding, solvation modeling, hydrophobic effect, new materials, integral equation theory, molecular dynamics, monte carlo simulations, quantum chemistry, water modeling, alcohols, liquids, critical points
Additional affiliations
October 1998 - July 2016
University of Ljubljana
Position
  • Professor (Full)
Education
October 1993 - September 1998
University of Ljubljana
Field of study
  • physics

Publications

Publications (93)
Article
We have developed an analytical theory for a simple model of liquid water. We apply Wertheim's thermodynamic perturbation theory (TPT) and integral equation theory (IET) for associative liquids to the rose model, which is among the simplest models of water. The particles interact through rose potentials for orientation dependent pairwise interactio...
Article
Full-text available
The thermodynamic and structural properties of the 2D hexagonal soft-sites fluid are examined by integral equation theory benchmarked against extensive Monte Carlo simulations. Hexamers are built of six equal Lennard-Jones segments. Site-site integral equation theory is used to compute site–site correlation functions, excess internal energies and i...
Article
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DNA sequences that are rich in guanines and can form four-stranded structures are called G-quadruplexes. Due to the growing evidence that they may play an important role in several key biological processes, the G-quadruplexes have captured the interest of several researchers. G-quadruplexes may form in the presence of different metal cations as pol...
Article
We have developed isothermal-isobaric algorithm for non-equilibrium Monte Carlo simulations. As first we have shown that the new method correctly predict density by comparing it to the density determined in canonical Monte Carlo simulations through the virial pressure. The new method was then used to study the effect of translational and rotational...
Preprint
Full-text available
We modelled the aqueous solvation of a nonpolar solute as a function of the radius, temperature and pressure. In this study a simple two-dimensional Mercedes-Benz (MB) water model was used in NPT Monte Carlo simulations. This model has previously been shown to qualitatively predict the volume anomalies of pure water and the free energy, enthalpy, e...
Article
We modelled the aqueous solvation of a nonpolar solute as a function of the radius, temperature and pressure. In this study a simple two-dimensional Mercedes-Benz (MB) water model was used in NPT Monte Carlo simulations. This model has previously been shown to qualitatively predict the volume anomalies of pure water and the free energy, enthalpy, e...
Article
Full-text available
The structures and properties of biomolecules like proteins, nucleic acids, and membranes depend on water. Water is also very important in industry. Overall, water is an unusual substance with more than 70 anomalous properties. The understanding of water is advancing significantly due to the theoretical and computational modeling. There are differe...
Article
Monte Carlo simulations, molecular dynamics and integral equation theory were used to study the thermodynamics and structure of particles interacting through the core softened interaction. Core-softened disks have two length scales of interaction, a hard core with one diameter and a soft corona with a larger diameter. We checked the possibility tha...
Article
Full-text available
Monte Carlo simulations and integral equation theory were used to study the thermodynamics and structure of mixture of particles interacting through the smooth version of Stell–Hemmer interaction and non-polar particles interacting through Lennard–Jones interaction in two dimensions. The theoretical results are tested against the Monte Carlo comput...
Article
We have studied the effect of rotational and translational degrees of freedom on solvation of nonpolar solutes. In this study a simple two-dimensional Mercedes-Benz (MB) water model was used. By separating temperature on rotational and translational part, the effect of different degrees of freedom on solvation was investigated. Increasing rotationa...
Article
The lattice Boltzmann method (LBM) is a computational method for a wide variety of fluid flow and multi-physics phenomena. These include systems governed by reaction-diffusion and reaction-diffusion-advection equations which are of major interest in many scientific and engineering fields. Typically, reactions are incorporated into LBM by means of a...
Article
A goal in computational chemistry is computing hydration free energies of nonpolar and charged solutes accurately, but with much greater computational speeds than in today's explicit-water simulations. Here, we take one step in that direction: a simple model of solvating waters that is analytical and thus essentially instantaneous to compute. Each...
Article
We developed a fast theory for studying how the rotational temperature (and rotational degrees of freedom) affects the properties of a simple model of liquid water. Wertheim's Thermodynamic perturbation theory (TPT) for associative liquids was applied to the Mercedes-Benz (MB) model. 2D MB model is one of the simplest models of water. The MB partic...
Article
Full-text available
The modelling-based design of microfluidic devices leads to highly efficient process intensification, which provides insights into different temporal and spatial scales at which processes in various fields of application could be performed. This requires not only an understanding of the underlying mechanisms of different processes at the micro scal...
Article
We developed an analytical theory for studying of rotational degrees of freedom of a simple model of liquid water. Wertheim's integral equation theory (IET) for associative liquids was applied to the Mercedes-Benz (MB) model, which is among the simplest models of water. The MB water molecules are modeled as 2-dimensional Lennard-Jones disks with th...
Article
In this work, the lattice Boltzmann (LB) method was applied to simulate incompressible steady and unsteady low Reynolds number (Re) flows around a confined cylinder. In the LB method, different collision models (Bhatnagar–Gross–Krook model, two-relaxation-time model, multi-relaxation-time model, and entropic lattice Boltzmann model) and a regulariz...
Article
In this manuscript, we develop a two-dimensional coarse-grained model to study equilibrium properties of fibril-like structures made of amyloid proteins. The phase space of the model is sampled using Monte Carlo computer simulations. At low densities and high temperatures proteins are mostly present as monomers while at low temperatures and high de...
Article
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The behavior of water, methanol, and water-methanol mixtures confined in narrow slit graphite pores as a function of pore size was investigated by Monte Carlo, hybrid Monte Carlo, and Molecular Dynamics simulations. Interactions were described using TIP4P/2005 for water, OPLS/2016 for methanol, and cross interactions fitted to excess water/methanol...
Article
Liquid water is considered poorly understood. How are water's physical properties encoded in its molecular structure? We introduce a statistical mechanical model (CageWater) of water's hydrogen bonding (HB) and Lennard-Jones (LJ) interactions. It predicts the energetic and volumetric and anomalous properties accurately. Yet, because the model is an...
Article
We investigate by Monte Carlo simulations density, diffusion, and structural anomalies of the simple two-dimensional Mercedes-Benz (MB) model of water, which is a very simple toy model for explaining the origin of water properties. MB water molecules are modeled as two-dimensional Lennard-Jones disks, with three orientation-dependent hydrogen-bondi...
Article
The structures and properties of biomolecules, such as proteins, nucleic acids and membranes, depend on water. Water is also very important in industry. Overall, water is unusual substance with more than 70 anomalous properties. The understanding of water is advancing significantly due to theoretical and computational modelling. There are different...
Article
One of the most important electrostatic interactions between molecules is most definitely the hydrogen bond. Understanding the basis of this interaction may offer us the insight needed to understand its effect on the macroscopic scale. Hydrogen bonding is for example the reason for anomalous properties in compounds like water and naturally life as...
Article
Methanol is the simplest alcohol and possible energy carrier because it is easier to store than hydrogen and burns cleaner than fossil fuels. It is a colorless liquid, completely miscible with water and organic solvents and is very hygroscopic. Here, simple two-dimensional models of methanol, based on Mercedes–Benz (MB) model of water, are examined...
Article
Full-text available
Two-dimensional ionic liquids with single site anion and cation-neutral dimer are studied by computer simulations and integral equation techniques, with the aim of characterizing differences with single site anion-cation mixtures, and also with three dimensional equivalents of both models, in order to see the competition between the Coulomb interac...
Article
Monte Carlo simulations of Mercedes-Benz water in a crowded environment were performed. The simulated systems are representative of both composite, porous or sintered materials and living cells with typical matrix packings. We studied the influence of overall temperature as well as the density and size of matrix particles on water density, particle...
Article
The structural properties of model two-dimensional (2D) ionic liquids are examined, with a particular focus on the charge ordering process, with the use of computer simulation and integral equation theories. The influence of the logarithmic form of the Coulomb interaction, versus that of a 3D screened interaction form, is analysed. Charge order is...
Article
In this paper we propose a model for the two dimensional fluid with one site-site associating point. We studied its structural and thermodynamic properties by the Monte Carlo computer simulations, the site-site integral equation theory (RISM), the Wertheim's thermodynamic perturbation theory (TPT) and the Wertheim's integral equation theory (WIET)...
Article
Monte Carlo simulations and Wertheim's thermodynamic perturbation theory (TPT) are used to predict the phase diagram and percolation curve for the simple two-dimensional Mercedes-Benz (MB) model of water. The MB model of water is quite popular for explaining water properties, but the phase diagram has not been reported till now. In the MB model, wa...
Article
Full-text available
We develop an analytical statistical-mechanical model for hydrophobic solvation in water. In this three-dimensional Mercedes-Benz–like model, two neighboring waters have three possible interaction states: a radial van der Waals interaction, a tetrahedral orientation-dependent hydrogen-bonding interaction, or no interaction. Nonpolar solutes are mod...
Article
Microreactor technology (MRT) has advantages, which can be efficiently used in the large scale manufacturing of chemicals. For economical and practical reasons, single microreactor unit has to be optimized before numbering up. In this paper, we carry out preliminary calculations for the selection of the optimal device dimensions for the case study...
Article
The major advantage of microreactor technology (MRT), reflected in high intensification of chemical and biochemical processes, arises from short diffusion paths in the microfluidic devices. However, the greatest opportunities and challenges still lie in the transfer of MRT to a real industrial environment. In this work we summarize commercial solut...
Article
Full-text available
In this paper we applied analytical theories for the two dimensional chain-forming fluid. Wertheims thermodynamic perturbation theory (TPT) and integral equation theory (IET) for associative liquids were used to study thermodynamical and structural properties of the chain-forming model. The model has polymerizing points at arbitrary position from c...
Article
Integral equation theories and Monte?Carlo simulations were used to determine the thermodynamic and structural properties of a two-dimensional asymmetric Coulomb system. We check correctness of different closures in integral equations and their ability to reproduce Kosterlitz?Thouless and vapour?liquid phase transitions of the electrolyte and criti...
Article
Non–equilibrium Monte Carlo and molecular dynamics simulations are used to study the effect of translational and rotational degrees of freedom on the structural and thermodynamic properties of the simple Mercedes–Benz water model. We establish a non–equilibrium steady state where rotational and translational temperatures can be tuned. We separately...
Article
In this manuscript we use a two-dimensional coarse-grained model to study how amyloid fibrils grow towards an equilibrium state where they coexist with proteins dissolved in a solution. Free-energies to dissociate proteins from fibrils are estimated from the residual concentration of dissolved proteins. Consistent with experiments, the concentratio...
Chapter
The commonly used macroscale techniques based on the continuum approximation cannot always be readily adapted to describe chemical reactions and transport processes that take place at the microscale. By contrast, particle-based mesoscale methods possess the unique ability to model relatively large physical systems, and, at the same time, effectivel...
Article
Structural and thermodynamic properties of a planar heterogeneous soft dumbbell fluid are examined using Monte Carlo simulations and integral equation theory. Lennard-Jones particles of different sizes are the building blocks of the dimers. The site-site integral equation theory in two dimensions is used to calculate the site-site radial distributi...
Article
A statistical model for a simple three-dimensional Mercedes-Benz model of water was used to study phase diagrams. This model on a simple level describes the thermal and volumetric properties of waterlike molecules. A molecule is presented as a soft sphere with four directions in which hydrogen bonds can be formed. Two neighboring waters can interac...
Data
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Article
In this paper we propose extension of the second-order thermodynamic perturbation theory (TPT2) for the inverse patchy colloids (IPC) with arbitrary number of patches. The theory is used to study thermodynamical properties and liquid-gas phase behavior of the IPC model with one, two and three patches. To validate the accuracy of the TPT2 we compare...
Article
In this paper we applied an analytical theory for the two dimensional dimerising fluid. We applied Wertheims thermodynamic perturbation theory (TPT) and integral equation theory (IET) for associative liquids to the dimerising model with arbitrary position of dimerising points from center of the particles. The theory was used to study thermodynamica...
Article
Full-text available
Methanol and water rank among the most important liquids in modern world due to their versatile use. As water, methanol and their mixtures exhibit numerous anomalous properties, their description is challenging. The amphiphilic nature of methanol causes its aqueous solutions to have negative excess volume and enthalpy across the entire composition...
Article
Full-text available
Understanding the spatial folding of proteins from their amino acid sequences has an enormous potential in contemporary life sciences. The ability to predict secondary and tertiary structures from primary ones through the use of computers will enable a much faster and more efficient discovery of organic substances with therapeutic or otherwise bioa...
Article
Full-text available
The phase behavior and the fluid structure of coarse-grain models for alcohols are studied by means of reference interaction site model (RISM) theory and Monte Carlo simulations. Specifically, we model ethanol and 1-propanol as linear rigid chains constituted by three (trimers) and four (tetramers) partially fused spheres, respectively. Thermodynam...
Article
Using Monte Carlo computer simulations, hydrophobic effect for a non-polar particle with the diameter of a water molecule was studied in water, confined within a disordered matrix. Freely mobile two-dimensional Mercedes-Benz water was put in a disordered, but fixed, matrix of Lennard-Jones disks. Influence of temperature and matrix properties on th...
Article
Properties of superconducting and superfluid thin films, modeled as a two-dimensional classic Coulomb fluid, are connected to the molecular structure of the system. Monte Carlo simulations to explore structural properties and ordering in the classical two-dimensional Coulomb fluid were performed. The density dependence of translational order parame...
Article
Full-text available
A simple model is constructed to study the phase diagram and thermodynamic properties of methanol, which is described as a dimer of an apolar sphere mimicking the methyl group and a sphere with core-softened potential as the hydroxyl group. Performing classical Monte Carlo simulations, we obtained the phase diagram, showing a second critical point...
Article
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Thermodynamic and structural properties of a coarse-grained model of methanol are examined by Monte Carlo simulations and reference interaction site model (RISM) integral equation theory. Methanol particles are described as dimers formed from an apolar Lennard-Jones sphere, mimicking the methyl group, and a sphere with a core-softened potential as...
Article
Knowledge of water-water potential is important for an accurate description of water. Potential between two molecules depends upon the distance, relative orientation of each molecule and local environment. In simulation, water-water hydrogen bonds are handled by point-charge water potentials and by polarizable models. These models produce good resu...
Article
A simple and computationally inexpensive core-softened model, originally proposed by Franzese [G. Franzese, J. Mol. Liq. 136, 267 (2007)], was adopted to show that it exhibits properties of waterlike fluid and hydrophobic effect. The potential used between particles is spherically symmetric with two characteristic lengths. Thermodynamics of nonpola...
Article
Monte Carlo simulations and integral equation theory were used to predict the thermodynamics and structure of a two-dimensional Coulomb fluid. We checked the possibility that integral equations reproduce Kosterlitz-Thouless and vapor-liquid phase transitions of the electrolyte and critical points. Integral equation theory results were compared to M...
Article
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In this work we focus on anti-parallel β-sheets to study hydration of side chains and polar groups of the backbone using all-atom molecular dynamics simulations. We show that: (i) water distribution around the backbone does not depend significantly on amino acid sequence, (ii) more water molecules are found around oxygen than nitrogen atoms of the...
Article
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Using Monte Carlo computer simulations, we show that a simple isotropic water-like model with two characteristic lengths can reproduce the hydrophobic effect and the solvation properties of small and large non-polar solutes. Influence of temperature, pressure, and solute size on the thermodynamic properties of apolar solute solvation in a water mod...
Article
The thermodynamic and structural properties of the planar soft-sites dumbbell fluid are examined by Monte Carlo simulations and integral equation theory. The dimers are built of two Lennard-Jones segments. Site-site integral equation theory in two dimensions is used to calculate the site-site radial distribution functions for a range of elongations...
Article
The Wertheim's integral equation theory was tested against newly obtained Monte Carlo computer simulations to describe the potential of mean force between two hydrophobic particles. An excellent agreement was obtained between the theoretical and simulation results. Further, the Wertheim's integral equation theory with polymer Percus-Yevick closure...
Article
The phase diagram of the two-dimensional particles interacting through a smooth version of Stell-Hemmer interaction was studied using Monte Carlo computer simulations. By evaluating the pressure-volume isotherms, we observed liquid-liquid, liquid-gas phase transitions and three stable crystal phases. The model shows the liquid-liquid critical point...
Article
Monte Carlo simulations and integral equation theory were used to study the thermodynamics and structure of particles interacting through the smooth version of Stell-Hemmer interaction. We checked the possibility that a fluid with a core-softened potential reproduces anomalies of liquid water such as the density anomaly, the minimum in the isotherm...
Article
An interaction model with core-softened potential in three dimensions was studied by Monte Carlo computer simulations and integral equation theory. We investigated the possibility that a fluid with a core-softened potential can reproduce anomalies found experimentally in liquid water, such as the density anomaly, the minimum in the isothermal compr...
Article
Water confined by the presence of a ‘sea’ of inert obstacles was examined. In the article, freely mobile two-dimensional Mercedes-Benz (MB) water put to a disordered, but fixed, matrix of Lennard-Jones disks was studied by the Monte Carlo computer simulations. For the MB water molecules in the matrix of Lennard-Jones disks, we explored the structur...
Article
The thermodynamic perturbation theory was tested against newly obtained Monte Carlo computer simulations to describe the major features of the hydrophobic effect in a simple 3D-Mercedes-Benz water model: the temperature and hydrophobe size dependence on entropy, enthalpy, and free energy of transfer of a simple hydrophobic solute into water. An exc...
Article
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Integral equation approaches, based on the Ornstein-Zernike equation, provide a fast way to calculate phase diagrams and thermodynamic properties of systems as opposed to time-consuming and computationally expensive computer simulations. However, when employing integral equations it is necessary to introduce simplifications. The Ornstein-Zernike eq...
Article
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Thermodynamic properties of the particles interacting through smooth version of Stell-Hemmer interaction were studied using Wertheim’s thermodynamic perturbation theory. The temperature dependence of molar volume, heat capacity, isothermal compressibility and thermal expansion coefficient at constant pressure for different number of bonding sites o...
Article
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The solvation free energies of ions are often computed using continuum theories, like the Born model. The Born model has the disadvantages that to fit experimental data, ionic radii are taken as adjustable parameters and you need to know the dielectric constant. We present here a more microscopic treatment for computing the free energies of ion sol...
Article
Full-text available
We developed a statistical model which describes the thermal and volumetric properties of water-like molecules. A molecule is presented as a three-dimensional sphere with four hydrogen-bonding arms. Each water molecule interacts with its neighboring waters through a van der Waals interaction and an orientation-dependent hydrogen-bonding interaction...
Article
Water is an unusual liquid in its solvation properties. Here, we model the process of transferring a nonpolar solute into water. Our goal was to capture the physical balance between water's hydrogen bonding and van der Waals interactions in a model that is simple enough to be nearly analytical and not heavily computational. We develop a 2-dimension...
Article
Full-text available
In-depth knowledge of water-water potential is important for devising and evaluating simple water models if they are to accurately describe water properties and reflect various solvation phenomena. Water-water potential depends upon inter-molecular distance, relative orientation of water molecules, and also local environment. When placed at a favor...
Article
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Ab stract Accuracy of different simple interaction site water models was tested. Instead of assessing their quality through the cal-culations of various water physical properties (dipole moment, dielectric constant, phase-equilibria diagrams, etc.) and comparison with experimental values, we calculated water-water potential and compared it with the...
Article
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Uni ver sity of Ljub lja na, De part ment of Che mi stry and Che mi cal En gi nee ring, Chair of Physi cal Che mi stry, A{ker~eva 5, SI-1000 Ljub lja na, Slo ve nia Ab stract Accuracy of different simple interaction site water models was tested. Instead of assessing their quality through the cal-culations of various water physical properties (dipol...
Article
Full-text available
mi stry and Che mi cal Tech no logy, Uni ver sity of Ljub lja na, As ker ce va 5, SI-1000, Slo ve ni 2 Lau fer Cen ter for Physi cal and Quan ti ta ti ve Bio logy, Stony Brook Uni ver sity, Ab stract The solvation free energies of ions are often computed using continuum theories, like the Born model. The Born model has the disadvantages that to fit...
Article
Full-text available
Associative version of Henderson-Abraham-Barker theory is applied for the study of Mercedes-Benz model of water near hydrophobic surface. We calculated density profiles and adsorption coefficients using Percus-Yevick and soft mean spherical associative approximations. The results are compared with Monte Carlo simulation data. It is shown that at hi...
Article
Full-text available
We develop a statistical mechanical model for the thermal and volumetric properties of waterlike fluids. Each water molecule is a two-dimensional disk with three hydrogen-bonding arms. Each water interacts with neighboring waters through a van der Waals interaction and an orientation-dependent hydrogen-bonding interaction. This model, which is larg...
Article
Full-text available
The two-dimensional Mercedes-Benz (MB) model of water has been widely studied, both by Monte Carlo simulations and by integral equation methods. Here, we study the three-dimensional (3D) MB model. We treat water as spheres that interact through Lennard-Jones potentials and through a tetrahedral Gaussian hydrogen bonding function. As the "right answ...
Data
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The thermodynamic perturbation approach and the cell theory are used to determine the complete phase diagram of a system of particles interacting via the Lennard-Jones potential. The Barker-Henderson perturbation theory (J. A. Barker, D. Henderson, J. Chem. Phys. 1967, 47, 4714–4721) is invoked to calculate the liquid-vapour line, while the cell mo...
Article
The viscosity of aqueous solutions of cesium fullerenehexamalonate T h -C 66(COOCs) 12, a rigid spherical nanometer-sized polyvalent salt, was measured by the Ubbelohde-type viscometer. The measurements were performed without added salt at 25 degrees C in the concentration range between 7 and 320 g/dm (3). THe concentration dependence of the obtain...
Data
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We perform all-atom computer simulations on nearly one hundred 6-, 8-, 10-, and 12-mer peptide fragments of protein G, and look for stable states. We simulated by replica-exchange molecular dynamics using Amber7 with the parm96 force-field and a GB/SA (generalized-Born/solvent accessible) implicit solvent model. We find that useful diagnostics for...
Article
Full-text available
We perform all-atom computer simulations on nearly one hundred 6-, 8-, 10-, and 12-mer peptide fragments of protein G, and look for stable states. We simulated by replica-exchange molecular dynamics using Amber7 with the parm96 force-field and a GB/SA (generalized-Born/solvent accessible) implicit solvent model. We find that useful diagnostics for...
Article
Full-text available
We recently developed an angle-dependent Wertheim integral equation theory (IET) of the Mercedes-Benz (MB) model of pure water [Silverstein et al., J. Am. Chem. Soc. 120, 3166 (1998)]. Our approach treats explicitly the coupled orientational constraints within water molecules. The analytical theory offers the advantage of being less computationally...
Article
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We previously applied Wertheim's thermodynamic perturbation theory for associative fluids to the simple Mercedes-Benz model of water. We found that the theory reproduced well the physical properties of hot water, but was less successful in capturing the more structured hydrogen bonding that occurs in cold water. Here, we propose an improved version...