69 citations · 216 across the 23 of their papers we have counts for
24 papers
Space-filling discrete helices
Jayanth R. Banavar, Achille Giacometti, Trinh X. Hoang +2
Proteins are linear chain molecules that play a central role in life and health. Protein native state folds are modular assemblies of space-filling building blocks of α-helices, \{…
Solvent Quality and Nonbiological Oligomer Folding: Revisiting Conventional Paradigms
Cedrix J. Dongmo Foumthuim, Tobia Arcangeli, Tatjana Škrbić +1
We report on extensive molecular dynamics atomistic simulations of a \textit{meta}-substituted \textit{poly}-phenylacetylene (pPA) foldamer dispersed in three solvents, water \ce{H…
Phase behaviour and self-assembly of semiflexible polymers in poor-solvent solutions
Tobia Arcangeli, Tatjana Škrbić, Somiealo Azote +6
Using Langevin dynamics complemented by Wang-Landau Monte Carlo simulations, we study the phase behavior of single and multiple semiflexible polymer chains in solution under poor-s…
Amino acid characteristics in protein native state structures
Tatjana Škrbić, Achille Giacometti, Trinh X. Hoang +2
We present a geometrical analysis of the protrusion statistics of side chains in more than 4,000 high-resolution protein structures. We employ a coarse-grained representation of th…
III. Geometrical framework for thinking about globular proteins: turns in proteins
Tatjana Škrbić, Achille Giacometti, Trinh X. Hoang +2
We have shown recently that the notion of poking pairwise interactions along a chain provides a unifying framework for understanding the formation of both secondary and the tertiar…
II. Geometrical framework for thinking about globular proteins: the power of poking
Tatjana Škrbić, Achille Giacometti, Trinh X. Hoang +2
Recently, we presented a framework for understanding protein structure based on the idea that simple constructs of holding hands or touching of objects can be used to rationalize t…
A geometrical framework for thinking about proteins
Jayanth R. Banavar, Achille Giacometti, Trinh X. Hoang +2
We present a model, based on symmetry and geometry, for proteins. Using elementary ideas from mathematics and physics, we derive the geometries of discrete helices and sheets. We p…
Proteins -- a celebration of consilience
Tatjana Škrbić, Trinh Xuan Hoang, Achille Giacometti +2
Proteins are the common constituents of all living cells. They are molecular machines that interact with each other as well as with other cell products and carry out a dizzying arr…
Marginally compact phase and ordered ground states in a model polymer with side spheres
Tatjana Škrbić, Trinh Xuan Hoang, Achille Giacometti +2
We present the results of a quantitative study of the phase behavior of a model polymer chain with side spheres using two independent computer simulation techniques. We find that t…
Spontaneous dimensional reduction and novel ground state degeneracy in a simple chain model
Tatjana Škrbić, Trinh Xuan Hoang, Achille Giacometti +2
Chain molecules play a key role in the polymer field and in living cells. Our focus is on a new homopolymer model of a linear chain molecule subject to an attractive self-interacti…
Local sequence-structure relationships in proteins
Tatjana Škrbić, Amos Maritan, Achille Giacometti +1
We seek to understand the interplay between amino acid sequence and local structure in proteins. Are some amino acids unique in their ability to fit harmoniously into certain local…
Building blocks of protein structures -- Physics meets Biology
Tatjana Škrbić, Amos Maritan, Achille Giacometti +2
The native state structures of globular proteins are stable and well-packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions…
Can the roles of polar and non-polar moieties be reversed in non-polar solvents?
Cedrix J. Dongmo, Manuel Carrer, Marine Houvet +3
Using thermodynamics integration, we study the solvation free energy of 18 amino acid side chain equivalents in solvents with different polarity, ranging from the most polar water…
Can Polarity-Inverted Surfactants Self-Assemble in Nonpolar Solvents
M. Carrer, T. Skrbic, S. L. Bore +3
We investigate the self-assembly process of a surfactant with inverted polarity in water and cyclohexane using both all-atom and coarse grained hybrid particle-field molecular dyna…
An integrated DEM-FEM approach to study breakage in packing of glass cartridges on a conveyor belt
Daniela Boso, Tommaso Braga, Simone Ravasini +6
The use of glass for pharmaceutical new applications such as high-technology drugs, requires the strictest container inertness. A common theme of paramount importance in glass cont…
Chain stiffness bridges conventional polymer and bio-molecular phases}
Tatjana Skrbic, Jayanth R. Banavar, Achille Giacometti
Chain molecules play important roles in industry and in living cells. Our focus here is on distinct ways of modeling the stiffness inherent in a chain molecule. We consider three t…
Local symmetry determines the phases of linear chains: a simple model for the self-assembly of peptide
Tatjana Skrbic, Trinh X. Hoang, Amos Maritan +2
We discuss the relation between the emergence of new phases with broken symmetry within the framework of simple models of biopolymers. We start with a classic model for a chain mol…
The elixir phase of chain molecule
Tatjana Škrbić, Trinh X. Hoang, Amos Maritan +2
A phase of matter is a familiar notion for inanimate physical matter. The nature of a phase of matter transcends the microscopic material properties. For example, materials in the…
Universal effects of solvent species on the stabilized structure of a protein
Tomohiko Hayashi, Masao Inoue, Emanuele Petretto +3
We investigate the effects of solvent specificities on the stability of the native structure (NS) of a protein on the basis of our free-energy function (FEF). We use CPB-bromodomai…
Effective stiffness and formation of secondary structures in a protein-like model
Tatjana Skrbic, Trinh X. Hoang, Achille Giacometti
We use Wang-Landau and replica exchange techniques to study the effect of an increasing stiffness on the formation of secondary structures in protein-like systems. Two possible mod…
From polymers to proteins: effect of side chains and broken symmetry in the formation of secondary structures within a Wang-Landau approach
Tatjana Škrbić, Artem Badasyan, Trinh Xuan Hoang +2
We study the equilibrium properties of a single flexible homopolymers where consecutive monomers are represented by impenetrable hard spherical beads tangential to each other, and…
Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field
Silvio a Beccara, Tatjana Skrbic, Roberto Covino +2
We report on atomistic simulation of the folding of a natively-knotted protein, MJ0366, based on a realistic force field. To the best of our knowledge this is the first reported ef…
The Role of Non-native Interactions in the Folding of Knotted Proteins
T. Skrbic, C. Micheletti, P. Faccioli
Stochastic simulations of coarse-grained protein models are used to investigate the propensity to form knots in early stages of protein folding. The study is carried out comparativ…
Dominant Folding Pathways of a WW Domain
S. a Beccara, T. Skrbic, R. Covino +1
We investigate the folding mechanism of the WW domain Fip35 using a realistic atomistic force field by applying the Dominant Reaction Pathways (DRP) approach. We find evidence for…