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- Alan Bizjak, Tomaž Urbič, Vojko Vlachy, Ken A. Dill
- The Journal of chemical physics
- 2009

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 answer," we… (More)

- Tomaž Urbič, Vojko Vlachy, Ken A. Dill
- The journal of physical chemistry. B
- 2006

We study water that is confined within small geometric spaces. We use the Mercedes-Benz (MB) model of water, in NVT and muVT Monte Carlo computer simulations. For MB water molecules between two planes separated by a distance d, we explore the structures, hydrogen bond networks, and thermodynamics as a function of d, temperature T, and water chemical… (More)

- Tomaž Urbič, C. L. Dias
- The Journal of chemical physics
- 2014

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 backbone,… (More)

- Tomaž Urbič, Vojko Vlachy, Yurij V Kalyuzhnyi, Ken A. Dill
- The Journal of chemical physics
- 2007

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… (More)

- Miha Lukšič, Tomaž Urbič, Barbara Hribar-Lee, Ken A. Dill
- The journal of physical chemistry. B
- 2012

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-dimensional… (More)

- Klemen Kržišnik, Tomaž Urbič
- Acta chimica Slovenica
- 2015

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 bioactive… (More)

- Tomaž Urbič
- Physical review. E, Statistical, nonlinear, and…
- 2012

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. This… (More)

- Tomaz Mohoric, Tomaž Urbič, Barbara Hribar-Lee
- The Journal of chemical physics
- 2013

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 excellent… (More)

- Tomaž Urbič
- The Journal of chemical physics
- 2013

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 isothermal… (More)

- Matej Huš, Tomaž Urbič
- Physical review. E, Statistical, nonlinear, and…
- 2014

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 between… (More)