arXiv subjects

Henri Orland

Publications and source records attributed to Henri Orland.

At least 37 records · Page 2Linked to original sources

arXiv2016

Improved RNA pseudoknots prediction and classification using a new topological invariant

We propose a new topological characterization of RNA secondary structures with pseudoknots based on two topological invariants. Starting from the classic arc-representation of RNA secondary structures, we consider a model that couples both I) the topological genus of the graph and II) the number of crossing arcs of the corresponding primitive graph. We add a term proportional to these topological invariants to the standard free energy of the RNA molecule, thus obtaining a novel free energy parametrization which takes into account the abundance of topologies of RNA pseudoknots observed in RNA databases.

q-bio.BM↗

arXiv2016

Beyond Poisson-Boltzmann: Numerical sampling of charge density fluctuations

We present a method aimed at sampling charge density fluctuations in Coulomb systems. The derivation follows from a functional integral representation of the partition function in terms of charge density fluctuations. Starting from the mean-field solution given by the Poisson-Boltzmann equation, an original approach is proposed to numerically sample fluctuations around it, through the propagation of a Langevin like stochastic partial differential equation (SPDE). The diffusion tensor of the SPDE can be chosen so as to avoid the numerical complexity linked to long-range Coulomb interactions, effectively rendering the theory completely local. A finite-volume implementation of the SPDE is described, and the approach is illustrated with preliminary results on the study of a system made of two like-charge ions immersed in a bath of counter-ions.

cond-mat.soft↗

arXiv2015

Phase behaviour of DNA in presence of DNA-binding proteins

To characterize the thermodynamical equilibrium of DNA chains interacting with a solution of non-specific binding proteins, a Flory-Huggins free energy model was implemented. We explored the dependence on DNA and protein concentrations of the DNA collapse. For physiologically relevant values of the DNA-protein affinity, this collapse gives rise to a biphasic regime with a dense and a dilute phase; the corresponding phase diagram was computed. Using an approach based on Hamiltonian paths, we show that the dense phase has either a molten globule or a crystalline structure, depending on the DNA bending rigidity, which is influenced by the ionic strength. These results are valid at the thermodynamical equilibrium and should therefore be consistent with many biological processes, whose characteristic timescales range typically from 1 ms to 10 s. Our model may thus be applied to biological phenomena that involve DNA-binding proteins, such as DNA condensation with crystalline order, which occurs in some bacteria to protect their chromosome from detrimental factors; or transcription initiation, which occurs in clusters called transcription factories that are reminiscent of the dense phase characterized in this study.

cond-mat.soft↗

arXiv2015

Effective Langevin equations for constrained stochastic processes

We propose a novel stochastic method to exactly generate Brownian paths conditioned to start at an initial point and end at a given final point during a fixed time $t_{f}$. These paths are weighted with a probability given by the overdamped Langevin dynamics. We show how these paths can be exactly generated by a local stochastic differential equation. The method is illustrated on the generation of Brownian bridges, Brownian meanders, Brownian excursions and constrained Ornstein-Uehlenbeck processes. In addition, we show how to solve this equation in the case of a general force acting on the particle. As an example, we show how to generate constrained path joining the two minima of a double-well. Our method allows to generate statistically independent paths, and is computationally very efficient.

cond-mat.stat-mech↗

arXiv2014

The unknotted strands of life: knots are very rare in RNA structures

The ongoing effort to detect and characterize physical entanglement in biopolymers has so far established that knots are present in many globular proteins and also abound in viral DNA packaged inside bacteriophages. RNA molecules, on the other hand, have not yet been systematically screened for the occurrence of physical knots. We have accordingly undertaken the systematic profiling of the ~6,000 RNA structures present in the protein data bank. The search identified no more than three deeply-knotted RNA molecules. These are ribosomal RNAs solved by cryo-em and consist of about 3,000 nucleotides. Compared to the case of proteins and viral DNA, the observed incidence of RNA knots is therefore practically negligible. This suggests that either evolutionary selection, or thermodynamic and kinetic folding mechanisms act towards minimizing the entanglement of RNA to an extent that is unparalleled by other types of biomolecules. The properties of the three observed RNA knotting patterns provide valuable clues for designing RNA sequences capable of self-tying in a twist-knot fold.

q-bio.BM↗

arXiv2013

Dynamics of Polymers: a Mean-Field Theory

We derive a general mean-field theory of inhomogeneous polymer dynamics; a theory whose form has been speculated and widely applied, but not heretofore derived. Our approach involves a functional integral representation of a Martin-Siggia-Rose type description of the exact many-chain dynamics. A saddle point approximation to the generating functional, involving conditions where the MSR action is stationary with respect to a collective density field $ρ$ and a conjugate MSR response field $ϕ$, produces the desired dynamical mean-field theory. Besides clarifying the proper structure of mean-field theory out of equilibrium, our results have implications for numerical studies of polymer dynamics involving hybrid particle-field simulation techniques such as the single-chain in mean-field method (SCMF).

cond-mat.soft↗

arXiv2013

Coherent States Formulation of Polymer Field Theory

We introduce a stable and efficient complex Langevin (CL) scheme to enable the first numerical simulations of the coherent-states (CS) formulation of polymer field theory. In contrast with Edwards' well known auxiliary-field (AF) framework, the CS formulation does not contain an embedded non-linear, non-local functional of the auxiliary fields, and the action of the field theory has a fully explicit, finite-order and semi-local polynomial character. In the context of a polymer solution model, we demonstrate that the new CS-CL dynamical scheme for sampling fluctuations in the space of coherent states yields results in good agreement with now-standard AF simulations. The formalism is potentially applicable to a broad range of polymer architectures and may facilitate systematic generation of trial actions for use in coarse-graining and numerical renormalization-group studies.

cond-mat.soft↗

arXiv2013

Dipolar Poisson-Boltzmann Approach to Ionic Solutions: A Mean Field and Loop Expansion Analysis

We study the variation of the dielectric response of ionic aqueous solutions as function of their ionic strength. The effect of salt on the dielectric constant appears through the coupling between ions and dipolar water molecules. On a mean-field level, we account for any internal charge distribution of particles. The dipolar degrees of freedom are added to the ionic ones and result in a generalization of the Poisson-Boltzmann (PB) equation called the Dipolar PB (DPB). By looking at the DPB equation around a fixed point-like ion, a closed-form formula for the dielectric constant is obtained. We express the dielectric constant using the "hydration length" that characterizes the hydration shell of dipoles around ions, and thus the strength of the dielectric decrement. The DPB equation is then examined for three additional cases: mixture of solvents, polarizable medium and ions of finite size. Employing field-theoretical methods we expand the Gibbs free-energy to first order in a loop expansion and calculate self-consistently the dielectric constant. For pure water, the dipolar fluctuations represent an important correction to the mean-field value and good agreement with the water dielectric constant is obtained. For ionic solutions we predict analytically the dielectric decrement that depends on the ionic strength in a non-linear way. Our prediction fits rather well a large range of concentrations for different salts using only one fit parameter related to the size of ions and dipoles. A linear dependence of the dielectric constant on the salt concentration is observed at low salinity, and a noticeable deviation from linearity can be seen for ionic strength above 1\,M, in agreement with experiments.

cond-mat.soft↗

arXiv2012

Tailoring Nanostructures Using Copolymer Nanoimprint Lithography

Finding affordable ways of generating high-density ordered nanostructures that can be transferred to a substrate is a major challenge for industrial applications like memories or optical devices with high resolution features. In this work, we report on a novel technique to direct self-assembled structures of block copolymers by NanoImprint Lithography. Surface energy of a reusable mold and nanorheology are used to organize the copolymers in defect-free structures over tens of micrometers in size. Versatile and controlled in-plane orientations of about 25 nm half-period lamellar nanostructures are achieved and, in particular, include applications to circular tracks of magnetic reading heads.

cond-mat.soft↗

arXiv2012

Block Copolymer at Nano-Patterned Surfaces

We present numerical calculations of lamellar phases of block copolymers at patterned surfaces. We model symmetric di-block copolymer films forming lamellar phases and the effect of geometrical and chemical surface patterning on the alignment and orientation of lamellar phases. The calculations are done within self-consistent field theory (SCFT), where the semi-implicit relaxation scheme is used to solve the diffusion equation. Two specific set-ups, motivated by recent experiments, are investigated. In the first, the film is placed on top of a surface imprinted with long chemical stripes. The stripes interact more favorably with one of the two blocks and induce a perpendicular orientation in a large range of system parameters. However, the system is found to be sensitive to its initial conditions, and sometimes gets trapped into a metastable mixed state composed of domains in parallel and perpendicular orientations. In a second set-up, we study the film structure and orientation when it is pressed against a hard grooved mold. The mold surface prefers one of the two components and this set-up is found to be superior for inducing a perfect perpendicular lamellar orientation for a wide range of system parameters.

cond-mat.soft↗

arXiv2012

Block Copolymer Films with Free Interfaces: Ordering by Nano-Patterned Substrates

We study block copolymers (BCP) on patterned substrates, where the top polymer film surface is not constrained but is a free interface that adapts its shape self-consistently. In particular, we investigate the combined effect of the free interface undulations with the wetting of the BCP film as induced by nano-patterned substrates. For a finite volume of BCP material, we find equilibrium droplets composed of coexisting perpendicular and parallel lamellar domains. The self-assembly of BCP on topographic patterned substrates was also investigated and it was found that the free interface induces mixed morphologies of parallel and perpendicular domains coupled with a non-flat free interface. In both cases, the free interface relaxes the strong constraints that would otherwise be imposed by a fixed top boundary (which is commonly used in simulations), and affects strongly the BCP ordering. Our study has some interesting consequences for experimental setups of graphoepitaxy and nanoimprint lithography.

cond-mat.soft↗

arXiv2012

The Dielectric Constant of Ionic Solutions: A Field-Theory Approach

We study the variation of the dielectric response of a dielectric liquid (e.g. water) when a salt is added to the solution. Employing field-theoretical methods we expand the Gibbs free-energy to first order in a loop expansion and calculate self-consistently the dielectric constant. We predict analytically the dielectric decrement which depends on the ionic strength in a complex way. Furthermore, a qualitative description of the hydration shell is found and is characterized by a single length scale. Our prediction fits rather well a large range of concentrations for different salts using only one fit parameter related to the size of ions and dipoles.

cond-mat.soft↗

arXiv2011

Secondary structure formation of homopolymeric single-stranded nucleic acids including force and loop entropy: implications for DNA hybridization

Loops are essential secondary structure elements in folded DNA and RNA molecules and proliferate close to the melting transition. Using a theory for nucleic acid secondary structures that accounts for the logarithmic entropy c ln m for a loop of length m, we study homopolymeric single-stranded nucleic acid chains under external force and varying temperature. In the thermodynamic limit of a long strand, the chain displays a phase transition between a low temperature / low force compact (folded) structure and a high temperature / high force molten (unfolded) structure. The influence of c on phase diagrams, critical exponents, melting, and force extension curves is derived analytically. For vanishing pulling force, only for the limited range of loop exponents 2 < c < 2.479 a melting transition is possible; for c <= 2 the chain is always in the folded phase and for 2.479 < c always in the unfolded phase. A force induced melting transition with singular behavior is possible for all loop exponents c < 2.479 and can be observed experimentally by single molecule force spectroscopy. These findings have implications for the hybridization or denaturation of double stranded nucleic acids. The Poland-Scheraga model for nucleic acid duplex melting does not allow base pairing between nucleotides on the same strand in denatured regions of the double strand. If the sequence allows these intra-strand base pairs, we show that for a realistic loop exponent c ~ 2.1 pronounced secondary structures appear inside the single strands. This leads to a lower melting temperature of the duplex than predicted by the Poland-Scheraga model. Further, these secondary structures renormalize the effective loop exponent c^, which characterizes the weight of a denatured region of the double strand, and thus affect universal aspects of the duplex melting transition.

cond-mat.stat-mech↗

arXiv2011

Generating Transition Paths by Langevin Bridges

We propose a novel stochastic method to generate paths conditioned to start in an initial state and end in a given final state during a certain time $t_{f}$. These paths are weighted with a probability given by the overdamped Langevin dynamics. We show that these paths can be exactly generated by a non-local stochastic differential equation. In the limit of short times, we show that this complicated non-solvable equation can be simplified into an approximate stochastic differential equation. For longer times, the paths generated by this approximate equation can be reweighted to generate the correct statistics. In all cases, the paths generated by this equation are statistically independent and provide a representative sample of transition paths. In case the reaction takes place in a solvent (e.g. protein folding in water), the explicit solvent can be treated. The method is illustrated on the one-dimensional quartic oscillator.

cond-mat.stat-mech↗

arXiv2011

A field-theoretic approach to nonequilibrium work identities

We study nonequilibrium work relations for a space-dependent field with stochastic dynamics (Model A). Jarzynski's equality is obtained through symmetries of the dynamical action in the path integral representation. We derive a set of exact identities that generalize the fluctuation-dissipation relations to non-stationary and far-from-equilibrium situations. These identities are prone to experimental verification. Furthermore, we show that a well-studied invariance of the Langevin equation under supersymmetry, which is known to be broken when the external potential is time-dependent, can be partially restored by adding to the action a term which is precisely Jarzynski's work. The work identities can then be retrieved as consequences of the associated Ward-Takahashi identities.

cond-mat.stat-mech↗

arXiv2011

Organization of Block Copolymers using NanoImprint Lithography: Comparison of Theory and Experiments

We present NanoImprint lithography experiments and modeling of thin films of block copolymers (BCP). The NanoImprint lithography is used to align perpendicularly lamellar phases, over distances much larger than the natural lamellar periodicity. The modeling relies on self-consistent field calculations done in two- and three-dimensions. We get a good agreement with the NanoImprint lithography setups. We find that, at thermodynamical equilibrium, the ordered BCP lamellae are much better aligned than when the films are deposited on uniform planar surfaces.

cond-mat.soft↗

arXiv2010

TT2NE: A novel algorithm to predict RNA secondary structures with pseudoknots

We present TT2NE, a new algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. TT2NE guarantees to find the minimum free energy structure irrespectively of pseudoknot topology. This unique proficiency is obtained at the expense of the maximum length of sequence that can be treated but comparison with state-of-the-art algorithms shows that TT2NE is a very powerful tool within its limits. Analysis of TT2NE's wrong predictions sheds light on the need to study how sterical constraints limit the range of pseudoknotted structures that can be formed from a given sequence. An implementation of TT2NE on a public server can be found at http://ipht.cea.fr/rna/tt2ne.php.

q-bio.BM↗

arXiv2010

Accelerated Stochastic Sampling of Discrete Statistical Systems

We propose a method to reduce the relaxation time towards equilibrium in stochastic sampling of complex energy landscapes in statistical systems with discrete degrees of freedom by generalizing the platform previously developed for continuous systems. The method starts from a master equation, in contrast to the Fokker-Planck equation for the continuous case. The master equation is transformed into an imaginary-time Schrödinger equation. The Hamiltonian of the Schrödinger equation is modified by adding a projector to its known ground state. We show how this transformation decreases the relaxation time and propose a way to use it to accelerate simulated annealing for optimization problems. We implement our method in a simplified kinetic Monte Carlo scheme and show an acceleration by an order of magnitude in simulated annealing of the symmetric traveling salesman problem. Comparisons of simulated annealing are made with the exchange Monte Carlo algorithm for the three-dimensional Ising spin glass. Our implementation can be seen as a step toward accelerating the stochastic sampling of generic systems with complex landscapes and long equilibration times.

cond-mat.stat-mech↗