arXiv subjects

Ranjan Mukhopadhyay

Publications and source records attributed to Ranjan Mukhopadhyay.

At least 19 recordsLinked to original sources

arXiv2024

The mind-brain relationship and the perspective of meaning

We view the mind-body problem in terms of the two interconnected problems of phenomenal consciousness and mental causation, namely, how subjective conscious experience can arise from physical neurological processes and how conscious mental states can causally act upon the physical world. In order to address these problems, I develop here a non-physicalist framework that combines two apparently antithetical views: the materialist view of the mind as a product of the brain and the metaphysical view of consciousness rooted in an underlying hidden reality. I discuss how this framework resolves the problem of mental causation while being simultaneously consistent with fundamental physical principles. I will elucidate how the framework ties in to the perspective of meaning that acts as the bridge between physical neurological processes and the conscious mind. Moreover, we will see how both our awareness of the self and our representation of the external world are connected to this perspective.

q-bio.NC↗

arXiv2018

Asymmetry between Activators and Deactivators in Functional Protein Networks

Are "turn-on" and "turn-off" functions in protein-protein interaction networks exact opposites of each other? To answer this question, we implement a minimal model for the evolution of functional protein-interaction networks using a sequence-based mutational algorithm, and apply the model to study neutral drift in networks that yield oscillatory dynamics. We study the roles of activators and deactivators, two core components of oscillatory protein interaction networks, and find a striking asymmetry in the roles of activating and deactivating proteins, where activating proteins tend to be synergistic and deactivating proteins tend to be competitive.

q-bio.MN↗

arXiv2018

Quantum mechanics, objective reality, and the problem of consciousness

The hard problem in consciousness is the problem of understanding how physical processes in the brain could give rise to subjective conscious experience. In this paper, I suggest that in order to understand the relationship between consciousness and the physical world, we need to probe deeply into the nature of physical reality. This leads us to quantum physics and to a second explanatory gap: that between quantum and classical reality. I will seek a philosophical framework that can address these two gaps simultaneously. Our analysis of quantum mechanics will naturally lead us to the notion of a hidden reality and to the postulate that consciousness is an integral component of this reality. The framework proposed in the paper provides the philosophical underpinnings for a theory of consciousness while satisfactorily resolving the interpretation problem in quantum mechanics without the need to alter its mathematical structure. I also discuss some implications for a scientific theory of consciousness.

physics.hist-ph↗

arXiv2017

Modeling Evolution of Crosstalk in Noisy Signal Transduction Networks

Signal transduction networks can form highly interconnected systems within cells due to network crosstalk, the sharing of input signals between multiple downstream responses. To better understand the evolutionary design principles underlying such networks, we study the evolution of crosstalk and the emergence of specificity for two parallel signaling pathways that arise via gene duplication and are subsequently allowed to diverge. We focus on a sequence based evolutionary algorithm and evolve the network based on two physically motivated fitness functions related to information transmission. Surprisingly, we find that the two fitness functions lead to very different evolutionary outcomes, one with a high degree of crosstalk and the other without.

physics.bio-ph↗

arXiv2017

Hidden long evolutionary memory in a model biochemical network

We introduce a minimal model for the evolution of functional protein-interaction networks using a sequence-based mutational algorithm, and apply the model to study neutral drift in networks that yield oscillatory dynamics. Starting with a functional core module, random evolutionary drift increases network complexity even in the absence of specific selective pressures. Surprisingly, we uncover a hidden order in sequence space that gives rise to long-term evolutionary memory, implying strong constraints on network evolution due to the topology of accessible sequence space.

q-bio.MN↗

arXiv2008

Exponential sensitivity of noise-driven switching in genetic networks

Cells are known to utilize biochemical noise to probabilistically switch between distinct gene expression states. We demonstrate that such noise-driven switching is dominated by tails of probability distributions and is therefore exponentially sensitive to changes in physiological parameters such as transcription and translation rates. However, provided mRNA lifetimes are short, switching can still be accurately simulated using protein-only models of gene expression. Exponential sensitivity limits the robustness of noise-driven switching, suggesting cells may use other mechanisms in order to switch reliably.

q-bio.MN↗

arXiv2008

Self-organized periodicity of protein clusters in growing bacteria

Chemotaxis receptors in E. coli form clusters at the cell poles and also laterally along the cell body, and this clustering plays an important role in signal transduction. Recently, experiments using flourrescence imaging have shown that, during cell growth, lateral clusters form at positions approximately periodically spaced along the cell body. In this paper, we demonstrate within a lattice model that such spatial organization could arise spontaneously from a stochastic nucleation mechanism. The same mechanism may explain the recent observation of periodic aggregates of misfolded proteins in E. coli.

cond-mat.stat-mech↗

arXiv2008

Particle-hole symmetry and the dirty boson problem

We study the role of particle-hole symmetry on the universality class of various quantum phase transitions corresponding to the onset of superfluidity at zero temperature of bosons in a quenched random medium. The functional integral formulation of this problem in d spatial dimensions yields a (d+1)-dimensional classical XY-model with extended disorder--the so-called random rod problem. Particle-hole symmetry may then be broken by adding nonzero site energies. We may distinguish three cases: (i) exact particle-hole symmetry, in which the site energies all vanish, (ii) statistical particle-hole symmetry in which the site energy distribution is symmetric about zero, vanishing on average, and (iii) complete absence of particle-hole symmetry in which the distribution is generic. We explore in each case the nature of the excitations in the non-superfluid Mott insulating and Bose glass phases. We find that the Bose glass compressibility, which has the interpretation of a temporal spin stiffness or superfluid density, is positive in cases (ii) and (iii), but that it vanishes with an essential singularity as full particle-hole symmetry is restored. We then focus on the critical point and discuss the relevance of type (ii) particle-hole symmetry breaking perturbations to the random rod critical behavior. We argue that a perturbation of type (iii) is irrelevant to the resulting type (ii) critical behavior: the statistical symmetry is restored on large scales close to the critical point, and case (ii) therefore describes the dirty boson fixed point. To study higher dimensions we attempt, with partial success, to generalize the Dorogovtsev-Cardy-Boyanovsky double epsilon expansion technique to this problem. The qualitative renormalization group flow picture this technique provides is quite compelling.

cond-mat.dis-nn↗

arXiv2007

Semi-soft Nematic Elastomers and Nematics in Crossed Electric and Magnetic Fields

Nematic elastomers with a locked-in anisotropy direction exhibit semi-soft elastic response characterized by a plateau in the stress-strain curve in which stress does not change with strain. We calculate the global phase diagram for a minimal model, which is equivalent to one describing a nematic in crossed electric and magnetic fields, and show that semi-soft behavior is associated with a broken symmetry biaxial phase and that it persists well into the supercritical regime. We also consider generalizations beyond the minimal model and find similar results.

cond-mat.soft↗

arXiv2007

Revisiting the dynamical exponent equality $z=d$ for the dirty boson problem

It is shown that previous arguments leading to the equality $z=d$ ($d$ being the spatial dimensionality) for the dynamical exponent describing the Bose glass to superfluid transition may break down, as apparently seen in recent simulations (Ref. \cite{Baranger}). The key observation is that the major contribution to the compressibility, which remains finite through the transition and was predicted to scale as $κ\sim |δ|^{(d-z)ν}$ (where $δ$ is the deviation from criticality and $ν$ is the correlation length exponent) comes from the analytic part, not the singular part of the free energy, and therefore is not restricted by any conventional scaling hypothesis.

cond-mat.dis-nn↗

arXiv2004

Optimal Path to Epigenetic Switching

We use large deviation methods to calculate rates of noise-induced transitions between states in multistable genetic networks. We analyze a synthetic biochemical circuit, the toggle switch, and compare the results to those obtained from a numerical solution of the master equation.

q-bio.MN↗

arXiv2003

Flexibility of beta-sheets: Principal-component analysis of database protein structures

Protein folds are built primarily from the packing together of two types of structures: alpha-helices and beta-sheets. Neither structure is rigid, and the flexibility of helices and sheets is often important in determining the final fold ({\it e.g.}, coiled coils and beta-barrels). Recent work has quantified the flexibility of alpha-helices using a principal-component analysis (PCA) of database helical structures (Emberly, 2003). Here, we extend the analysis to beta-sheet flexibility using PCA on a database of beta-sheet structures. For sheets of varying dimension and geometry, we find two dominant modes of flexibility: twist and bend. The distributions of amplitudes for these modes are found to be Gaussian and independent, suggesting that the PCA twist and bend modes can be identified as the soft elastic normal modes of sheets. We consider the scaling of mode eigenvalues with sheet size and find that parallel beta-sheets are more rigid than anti-parallel sheets over the entire range studied. Lastly, we discuss the application of our PCA results to modeling and design of beta-sheet proteins.

cond-mat.soft↗

arXiv2003

Statistical mechanics of RNA folding: importance of alphabet size

We construct a minimalist model of RNA secondary-structure formation and use it to study the mapping from sequence to structure. There are strong, qualitative differences between two-letter and four or six-letter alphabets. With only two kinds of bases, there are many alternate folding configurations, yielding thermodynamically stable ground-states only for a small set of structures of high designability, i.e., total number of associated sequences. In contrast, sequences made from four bases, as found in nature, or six bases have far fewer competing folding configurations, resulting in a much greater average stability of the ground state.

cond-mat.stat-mech↗

arXiv2003

Fluctuating Nematic Elastomer Membranes: a New Universality Class

We study the flat phase of nematic elastomer membranes with rotational symmetry spontaneously broken by in-plane nematic order. Such state is characterized by a vanishing elastic modulus for simple shear and soft transverse phonons. At harmonic level, in-plane orientational (nematic) order is stable to thermal fluctuations, that lead to short-range in-plane translational (phonon) correlations. To treat thermal fluctuations and relevant elastic nonlinearities, we introduce two generalizations of two-dimensional membranes in a three dimensional space to arbitrary D-dimensional membranes embedded in a d-dimensional space, and analyze their anomalous elasticities in an expansion about D=4. We find a new stable fixed point, that controls long-scale properties of nematic elastomer membranes. It is characterized by singular in-plane elastic moduli that vanish as a power-law eta_lambda=4-D of a relevant inverse length scale (e.g., wavevector) and a finite bending rigidity. Our predictions are asymptotically exact near 4 dimensions.

cond-mat.soft↗

arXiv2002

Flexibility of $α$-helices: Results of a statistical analysis of database protein structures

$α$-helices stand out as common and relatively invariant secondary structural elements of proteins. However, $α$-helices are not rigid bodies and their deformations can be significant in protein function ({\it e.g.} coiled coils). To quantify the flexibility of $α$-helices we have performed a structural principal-component analysis of helices of different lengths from a representative set of protein folds in the Protein Data Bank. We find three dominant modes of flexibility: two degenerate bend modes and one twist mode. The data are consistent with independent Gaussian distributions for each mode. The mode eigenvalues, which measure flexibility, follow simple scaling forms as a function of helix length. The dominant bend and twist modes and their harmonics are reproduced by a simple spring model, which incorporates hydrogen-bonding and excluded volume. As an application, we examine the amount of bend and twist in helices making up several coiled-coil proteins. Incorporation of $α$-helix flexibility into structure refinement and design is discussed.

cond-mat.stat-mech↗

arXiv2001

Symmetries and Elasticity of Nematic Gels

A nematic liquid-crystal gel is a macroscopically homogeneous elastic medium with the rotational symmetry of a nematic liquid crystal. In this paper, we develop a general approach to the study of these gels that incorporates all underlying symmetries. After reviewing traditional elasticity and clarifying the role of broken rotational symmetries in both the reference space of points in the undistorted medium and the target space into which these points are mapped, we explore the unusual properties of nematic gels from a number of perspectives. We show how symmetries of nematic gels formed via spontaneous symmetry breaking from an isotropic gel enforce soft elastic response characterized by the vanishing of a shear modulus and the vanishing of stress up to a critical value of strain along certain directions. We also study the phase transition from isotropic to nematic gels. In addition to being fully consistent with approaches to nematic gels based on rubber elasticity, our description has the important advantages of being independent of a microscopic model, of emphasizing and clarifying the role of broken symmetries in determining elastic response, and of permitting easy incorporation of spatial variations, thermal fluctuations, and gel heterogeneity, thereby allowing a full statistical-mechanical treatment of these novel materials.

cond-mat.soft↗

arXiv2001

The Fractional Quantum Hall effect in an array of quantum wires

We demonstrate the emergence of the quantum Hall (QH) hierarchy in a 2D model of coupled quantum wires in a perpendicular magnetic field. At commensurate values of the magnetic field, the system can develop instabilities to appropriate inter-wire electron hopping processes that drive the system into a variety of QH states. Some of the QH states are not included in the Haldane-Halperin hierarchy. In addition, we find operators allowed at any field that lead to novel crystals of Laughlin quasiparticles. We demonstrate that any QH state is the groundstate of a Hamiltonian that we explicitly construct.

cond-mat.mes-hall↗

arXiv2001

Sliding Luttinger liquid phases

We study systems of coupled spin-gapped and gapless Luttinger liquids. First, we establish the existence of a sliding Luttinger liquid phase for a system of weakly coupled parallel quantum wires, with and without disorder. It is shown that the coupling can {\it stabilize} a Luttinger liquid phase in the presence of disorder. We then extend our analysis to a system of crossed Luttinger liquids and establish the stability of a non-Fermi liquid state: the crossed sliding Luttinger liquid phase (CSLL). In this phase the system exhibits a finite-temperature, long-wavelength, isotropic electric conductivity that diverges as a power law in temperature $T$ as $T \to 0$. This two-dimensional system has many properties of a true isotropic Luttinger liquid, though at zero temperature it becomes anisotropic. An extension of this model to a three-dimensional stack exhibits a much higher in-plane conductivity than the conductivity in a perpendicular direction.

cond-mat.str-el↗