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Jayanth R. Banavar

Publications and source records attributed to Jayanth R. Banavar.

At least 55 records · Page 3Linked to original sources
arXiv2007

Structural motifs of biomolecules

Biomolecular structures are assemblies of emergent anisotropic building modules such as uniaxial helices or biaxial strands. We provide an approach to understanding a marginally compact phase of matter that is occupied by proteins and DNA. This phase, which is in some respects analogous to the liquid crystal phase for chain molecules, stabilizes a range of shapes that can be obtained by sequence-independent interactions occurring intra- and intermolecularly between polymeric molecules. We present a singularityfree self-interaction for a tube in the continuum limit and show that this results in the tube being positioned in the marginally compact phase. Our work provides a unified framework for understanding the building blocks of biomolecules.

q-bio.BM↗
arXiv2006

Geometry of proteins: hydrogen bonding, sterics and marginally compact tubes

The functionality of proteins is related to their structure in the native state. Protein structures are made up of emergent building blocks of helices and almost planar sheets. A simple coarse-grained geometrical model of a flexible tube barely subject to compaction provides a unified framework for understanding the common character of globular proteins.We argue that a recent critique of the tube idea is not well founded.

q-bio.BM↗
arXiv2006

Nanoscale fluid flows in the vicinity of patterned surfaces

Molecular dynamics simulations of dense and rarefied fluids comprising small chain molecules in chemically patterned nano-channels predict a novel switching from Poiseuille to plug flow along the channel. We also demonstrate behavior akin to the lotus effect for a nanodrop on a chemically patterned substrate. Our results show that one can control and exploit the behavior of fluids at the nanoscale using chemical patterning.

cond-mat.soft↗
arXiv2006

Slip, immiscibility and boundary conditions at the liquid-liquid interface

The conventional boundary conditions at the interface between two flowing liquids include continuity of the tangential velocity. We have tested this assumption with molecular dynamics simulations of Couette and Poiseuille flows of two-layered liquid systems, with various molecular structures and interactions. When the total liquid density near the interface drops significantly compared to the bulk values, the tangential velocity varies very rapidly there, and would appear discontinuous at continuum resolution. The value of this apparent slip is given by a Navier boundary condition.

cond-mat.soft↗
arXiv2005

Spatial Scaling in Model Plant Communities

We present an analytically tractable variant of the voter model that provides a quantitatively accurate description of beta-diversity (two-point correlation function) in two tropical forests. The model exhibits novel scaling behavior that leads to links between ecological measures such as relative species abundance and the species area relationship.

q-bio.PE↗
arXiv2005

Proteins and polymers

Proteins, chain molecules of amino acids, behave in ways which are similar to each other yet quite distinct from standard compact polymers. We demonstrate that the Flory theorem, derived for polymer melts, holds for compact protein native state structures and is not incompatible with the existence of structured building blocks such as $α$-helices and $β$-strands. We present a discussion on how the notion of the thickness of a polymer chain, besides being useful in describing a chain molecule in the continuum limit, plays a vital role in interpolating between conventional polymer physics and the phase of matter associated with protein structures.

q-bio.BM↗
arXiv2005

Geometrical model for the native-state folds of proteins

We recently introduced a physical model [Hoang et al., P. Natl. Acad. Sci. USA (2004), Banavar et al., Phys. Rev. E (2004)] for proteins which incorporates, in an approximate manner, several key features such as the inherent anisotropy of a chain molecule, the geometrical and energetic constraints placed by the hydrogen bonds and sterics, and the role played by hydrophobicity. Within this framework, marginally compact conformations resembling the native state folds of proteins emerge as broad competing minima in the free energy landscape even for a homopolymer. Here we show how the introduction of sequence heterogeneity using a simple scheme of just two types of amino acids, hydrophobic (H) and polar (P), and sequence design allows a selected putative native fold to become the free energy minimum at low temperature. The folding transition exhibits thermodynamic cooperativity, if one neglects the degeneracy between two different low energy conformations sharing the same fold topology.

q-bio.BM↗
arXiv2005

Neutral Theory and Relative Species Abundance in Ecology

The theory of island biogeography[1] asserts that an island or a local community approaches an equilibrium species richness as a result of the interplay between the immigration of species from the much larger metacommunity source area and local extinction of species on the island (local community). Hubbell[2] generalized this neutral theory to explore the expected steady-state distribution of relative species abundance (RSA) in the local community under restricted immigration. Here we present a theoretical framework for the unified neutral theory of biodiversity[2] and an analytical solution for the distribution of the RSA both in the metacommunity (Fisher's logseries) and in the local community, where there are fewer rare species. Rare species are more extinction-prone, and once they go locally extinct, they take longer to re-immigrate than do common species. Contrary to recent assertions[3], we show that the analytical solution provides a better fit, with fewer free parameters, to the RSA distribution of tree species on Barro Colorado Island (BCI)[4] than the lognormal distribution[5,6].

q-bio.PE↗
arXiv2004

Lattice tube model of proteins

We present a new lattice model for proteins that incorporates a tube-like anisotropy by introducing a preference for mutually parallel alignments in the conformations. The model is demonstrated to capture many aspects of real proteins.

q-bio.BM↗
arXiv2004

Unified perspective on proteins: A physics approach

We study a physical system which, while devoid of the complexity one usually associates with proteins, nevertheless displays a remarkable array of protein-like properties. The constructive hypothesis that this striking resemblance is not accidental leads not only to a unified framework for understanding protein folding, amyloid formation and protein interactions but also has implications for natural selection.

cond-mat.stat-mech↗
arXiv2004

Network Structures from Selection Principles

We present an analysis of the topologies of a class of networks which are optimal in terms of the requirements of having as short a route as possible between any two nodes while yet keeping the congestion in the network as low as possible. Strikingly, we find a variety of distinct topologies and novel phase transitions between them on varying the number of links per node. Our results suggest that the emergence of the topologies observed in nature may arise both from growth mechanisms and the interplay of dynamical mechanisms with a selection process.

cond-mat.stat-mech↗
arXiv2004

Geometry and symmetry presculpt the free-energy landscape of proteins

We present a simple physical model which demonstrates that the native state folds of proteins can emerge on the basis of considerations of geometry and symmetry. We show that the inherent anisotropy of a chain molecule, the geometrical and energetic constraints placed by the hydrogen bonds and sterics, and hydrophobicity are sufficient to yield a free energy landscape with broad minima even for a homopolymer. These minima correspond to marginally compact structures comprising the menu of folds that proteins choose from to house their native-states in. Our results provide a general framework for understanding the common characteristics of globular proteins.

q-bio.BM↗
arXiv2004

What one can learn from experiments about the elusive transition state?

We present the results of an exact analysis of a model energy landscape of a protein to clarify the notion of the transition state and the physical meaning of the $ϕ$ values determined in protein engineering experiments. We benchmark our findings to various theoretical approaches proposed in the literature for the identification and characterization of the transition state.

q-bio.BM↗
arXiv2003

Scaling and universality in ontogenetic growth

Recently, West et al. claimed to derive a general quantitative model based on fundamental principles for the allocation of metabolic energy between maintenance of existing tissue and the production of new biomass, and in addition claimed to derive a single, parameterless universal curve that describes the growth of many species. They further claimed that their model of the 3/4 exponent for the allometric scaling of metabolism provides a novel version of the growth equations and use the goodness of fit of growth-curve data to these equations as support of this interpretation. Here, we show that the universal curve arises from general considerations that are independent of the specific allometric model used and that the data do not distinguish between the 3/4 or the 2/3 exponent for the metabolic rate mass scaling.

cond-mat↗
arXiv2003

From polymers to proteins -- novel phases of short compact tubes

A framework is presented for understanding the common character of proteins. Proteins are linear chain molecules. However, the simple model of a polymer viewed as spheres tethered together does not account for many of the observed characteristics of protein structures. The authors show here that proteins may be regarded as tubes of nonzero thickness. This approach allows one to bridge the conventional compact polymer phase with a novel phase employed by Nature to house biomolecular structures. The continuum description of a tube (or a sheet) of arbitrary thickness entails using appropriately chosen many-body interactions rather than two-body interactions. The authors suggest that the structures of folded proteins are selected based on geometrical considerations and are poised at the edge of compaction, thus accounting for their versatility and flexibility. This approach also offers an explanation for why helices and sheets are the building blocks of protein structures.

cond-mat.stat-mech↗
arXiv2002

Molecular dynamics simulations of crystallization of hard spheres

We have carried out molecular dynamics simulations of the crystallization of hard spheres modelling colloidal systems that are studied in conventional and space-based experiments. We use microscopic probes to investigate the effects of gravitational forces, polydispersity and of bounding walls on the phase structure. The simulations employed an extensive exclusive particle grid method and the type and degree of crystalline order was studied in two independent ways: by the structure factor, as in experiments, and through local rotational invariants. We present quantitative comparisons of the nucleation rates of monodisperse and polydisperse hard sphere systems and benchmark them against experimental results. We show how the presence of bounding walls leads to wall-induced nucleation and rapid crystallization and discuss the role of gravity on the dynamics of crystallization.

cond-mat↗
arXiv2002

Effects of Pore Walls and Randomness on Phase Transitions in Porous Media

We study spin models within the mean field approximation to elucidate the topology of the phase diagrams of systems modeling the liquid-vapor transition and the separation of He$^3$--He$^4$ mixtures in periodic porous media. These topologies are found to be identical to those of the corresponding random field and random anisotropy spin systems with a bimodal distribution of the randomness. Our results suggest that the presence of walls (periodic or otherwise) are a key factor determining the nature of the phase diagram in porous media.

cond-mat.stat-mech↗