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Papers by Marcelo Marucho

Research paper thumbnail of Adsorption of Soft and Hard Proteins onto OTCEs under the Influence of an External Electric Field

Research paper thumbnail of Hydrodynamic and Polyelectrolyte Properties of Actin Filaments: Theory and Experiments

bioRxiv (Cold Spring Harbor Laboratory), Jan 12, 2022

Research paper thumbnail of Polyelectrolyte Nature of Cytoskeleton Filaments and Their Properties

Bulletin of the American Physical Society, Mar 8, 2018

Research paper thumbnail of Transformada de Borel Generalizada (TBG)

Facultad de Ciencias Exacta

Research paper thumbnail of Non-Borel summable Φ4 theory in zero dimension: A toy model for testing numerical and analytical methods

Journal of Mathematical Physics, Apr 1, 2008

The exact analytical solution for the generating functional of the zero-dimensional Φ4 theory wit... more The exact analytical solution for the generating functional of the zero-dimensional Φ4 theory with degenerate minima is obtained in the whole complex coupling parameter plane for testing purposes. The efficiency and precision of different computing tools, proposed in non-Borel summable field theories to obtain approximate solutions in both perturbative and nonperturbative regimes, are analyzed. Furthermore, a new resummation approach is proposed in order to successfully deal with factorially divergent series. It provides a representation of the generating function in terms of an unambiguously defined Laplace–Borel integral. On the other hand, a recent approach called the generalized Borel transform is shown to be an accurate and robust technique to capture non perturbative contributions in the coupling parameter. An extension of this approach to path integrals is proposed.

Research paper thumbnail of Solutions of the Optimized Closure Integral Equation Theory: Heteronuclear Polyatomic Fluids

Journal of Chemical Theory and Computation, Feb 21, 2008

Research paper thumbnail of CACPPAF, A COMSOL Application to Characterize Polyelectrolyte Properties of Actin Filaments

Social Science Research Network, 2022

Research paper thumbnail of Java application for cytoskeleton filament characterization (JACFC)

Software impacts, May 1, 2021

Research paper thumbnail of A java application to characterize biomolecules and nanomaterials in electrolyte aqueous solutions

Computer Physics Communications, Sep 1, 2019

Research paper thumbnail of MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations

Computer Physics Communications, 2016

Research paper thumbnail of Ion–ion correlation, solvent excluded volume and pH effects on physicochemical properties of spherical oxide nanoparticles

Journal of Colloid and Interface Science, 2016

Research paper thumbnail of Statistical mechanics of worm-like polymers from a new generating function

Journal of Chemical Physics, Sep 14, 2004

Research paper thumbnail of An optimized theory for charged macroions immersed in a molecular electrolyte

Bulletin of the American Physical Society, Mar 23, 2012

Research paper thumbnail of Statistical Mechanics of Semiflexible Polymer Chains from a new Generating Function

arXiv (Cornell University), Sep 26, 2003

In this paper, we present a new approach to the Kratky-Porod Model (KP) of semiflexible polymers.... more In this paper, we present a new approach to the Kratky-Porod Model (KP) of semiflexible polymers. Our solution to the model is based on the definition of a generating function which we use to study the statistical mechanics of semiflexible polymer chains. Specifically, we derive mathematical expressions for the characteristic function, the polymer propagator and the mean square end-to-end distance from the generating function. These expressions are valid for polymers with any number of segments and degree of rigidity. Furthermore, they capture the limits of fully flexible and stiff polymers exactly. In between, a smooth and approximate crossover behavior is predicted. The most important contribution of this paper is the expression of the polymer propagator which is written in a very simple and insightful way. It is given in terms of the exact polymer propagator of the Random Flight Model multiplied by an exponential that takes into account the stiffness of the polymer backbone.

Research paper thumbnail of Statistics of Semiflexible Polymer Chains and the Generalized Borel Transform

arXiv (Cornell University), Jun 30, 2003

In this paper, we present a new approach to the discrete version of the Wormlike Chain Model (WCM... more In this paper, we present a new approach to the discrete version of the Wormlike Chain Model (WCM) of semiflexible polymers. Our solution to the model is based on a new computational technique called the Generalized Borel Transform (GBT) which we use to study the statistical mechanics of semiflexible polymer chains. Specifically, we evaluate the characteristic function of the model approximately. Afterward, we compute the polymer propagator of the model using the GBT and find an expression valid for polymers with any number of segments and values of the semiflexibility parameter. This expression captures the limits of flexible and infinitely stiff polymers exactly. In between, a smooth and approximate crossover behavior is predicted. Another property of our propagator is that it fulfills the condition of finite extensibility of the polymer chain. We have also calculated the single chain structure factor. This property is a decreasing function of the wave vector, k,k,k, until a plateau is reached. Our computations clearly show that the structure factor decreases faster with increasing wave vector when the semiflexibility parameter is increased. Furthermore, when the wave vector is large enough, there is a regime where the structure factor follows an approximate power law of the form k−thetak^{-\theta}k−theta even for short polymer chains. theta\thetatheta is equal to two for flexible polymers and to one for rigid chains. We also compare our results to the predictions of other models.

Research paper thumbnail of Electrical impulse characterization along actin filaments in pathological conditions

bioRxiv (Cold Spring Harbor Laboratory), Sep 6, 2021

Research paper thumbnail of A Multi-Scale Approach to Describe Electrical Impulses Propagating along Actin Filaments in both Intracellular and In-vitro Conditions

arXiv (Cornell University), Jan 18, 2018

Research paper thumbnail of Simulations of RNA Interactions with Monovalent Ions

Methods in Enzymology, 2009

RNA folding and binding reactions are mediated by interactions with ions that make up the surroun... more RNA folding and binding reactions are mediated by interactions with ions that make up the surrounding aqueous electrolytic milieu. Although Mg(2+) ions are often implicated as being crucial for RNA folding, it is known that folding is feasible in high concentrations of monovalent alkali-halide salts. Experiments have yielded important information regarding the salt dependence of RNA stability. Recent work has shown that molecular simulations based on explicit representations of solvent molecules and monovalent ions can also provide useful insights regarding the ionic atmospheres around model RNA systems. These insights can help rationalize intriguing observations regarding the dependence of RNA stability on cation type providing one pays attention to important considerations that go into the proper design of molecular simulations. These issues are discussed in detail and the methods are applied to an A-form RNA and B-form DNA sequence. The results of these simulations are compared to previous work on a kissing-loop system with analogous sequence. In particular, ionic atmospheres obtained from molecular simulations are compared to those obtained using the nonlinear Poisson Boltzmann model for continuum electrostatics for these three different nucleic acid systems. The comparisons indicate reasonable agreement in terms of coarse-grained observables such as the numbers of counterions accumulated around the solutes. However, details of the ionic atmospheres, captured in terms of spatial free energy density profiles, are quite different between the two approaches. These comparisons suggest the need for improvements in continuum models to capture sequence-specific effects, ion-ion correlation, and the effects of partial dehydration of ions.

Research paper thumbnail of The Self-Adaptation Ability of Zinc Oxide Nanoparticles Enables Reliable Cancer Treatments

Nanomaterials, Feb 5, 2020

Research paper thumbnail of Suitability of the Method Of Lines for rendering analytic/numeric solutions of the unsteady heat conduction equation in a large plane wall with asymmetric convective boundary conditions

International Journal of Heat and Mass Transfer, Aug 1, 2016

Abstract The primary objective of the present study is to implement the Method Of Lines (MOL) for... more Abstract The primary objective of the present study is to implement the Method Of Lines (MOL) for the analysis of the unsteady, one-dimensional, heat conduction equation in a large plane wall with different convective boundary conditions at the two exposed surfaces. In the equation, MOL discretizes the space derivative while leaving the time derivative continuous. By way of MOL, the adjoint system of linear, first order ordinary differential equations will be solved analytically (not numerically) with the eigenvalue method. The outcome of the computational procedure provides a discrete sequence of piecewise temperatures-time variations at each line, which is expressed in terms of linear combinations of exponential functions of time containing the eigenvalues and eigenvectors. A practical example dealing with the temperature evolution in a large single-pane window is tackled with two meshes, one having three and the other having five lines. The collection of analytic/numeric temperature–time solutions provided by MOL and the eigenvalue method exhibits excellent quality at all time.

Research paper thumbnail of Adsorption of Soft and Hard Proteins onto OTCEs under the Influence of an External Electric Field

Research paper thumbnail of Hydrodynamic and Polyelectrolyte Properties of Actin Filaments: Theory and Experiments

bioRxiv (Cold Spring Harbor Laboratory), Jan 12, 2022

Research paper thumbnail of Polyelectrolyte Nature of Cytoskeleton Filaments and Their Properties

Bulletin of the American Physical Society, Mar 8, 2018

Research paper thumbnail of Transformada de Borel Generalizada (TBG)

Facultad de Ciencias Exacta

Research paper thumbnail of Non-Borel summable Φ4 theory in zero dimension: A toy model for testing numerical and analytical methods

Journal of Mathematical Physics, Apr 1, 2008

The exact analytical solution for the generating functional of the zero-dimensional Φ4 theory wit... more The exact analytical solution for the generating functional of the zero-dimensional Φ4 theory with degenerate minima is obtained in the whole complex coupling parameter plane for testing purposes. The efficiency and precision of different computing tools, proposed in non-Borel summable field theories to obtain approximate solutions in both perturbative and nonperturbative regimes, are analyzed. Furthermore, a new resummation approach is proposed in order to successfully deal with factorially divergent series. It provides a representation of the generating function in terms of an unambiguously defined Laplace–Borel integral. On the other hand, a recent approach called the generalized Borel transform is shown to be an accurate and robust technique to capture non perturbative contributions in the coupling parameter. An extension of this approach to path integrals is proposed.

Research paper thumbnail of Solutions of the Optimized Closure Integral Equation Theory: Heteronuclear Polyatomic Fluids

Journal of Chemical Theory and Computation, Feb 21, 2008

Research paper thumbnail of CACPPAF, A COMSOL Application to Characterize Polyelectrolyte Properties of Actin Filaments

Social Science Research Network, 2022

Research paper thumbnail of Java application for cytoskeleton filament characterization (JACFC)

Software impacts, May 1, 2021

Research paper thumbnail of A java application to characterize biomolecules and nanomaterials in electrolyte aqueous solutions

Computer Physics Communications, Sep 1, 2019

Research paper thumbnail of MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations

Computer Physics Communications, 2016

Research paper thumbnail of Ion–ion correlation, solvent excluded volume and pH effects on physicochemical properties of spherical oxide nanoparticles

Journal of Colloid and Interface Science, 2016

Research paper thumbnail of Statistical mechanics of worm-like polymers from a new generating function

Journal of Chemical Physics, Sep 14, 2004

Research paper thumbnail of An optimized theory for charged macroions immersed in a molecular electrolyte

Bulletin of the American Physical Society, Mar 23, 2012

Research paper thumbnail of Statistical Mechanics of Semiflexible Polymer Chains from a new Generating Function

arXiv (Cornell University), Sep 26, 2003

In this paper, we present a new approach to the Kratky-Porod Model (KP) of semiflexible polymers.... more In this paper, we present a new approach to the Kratky-Porod Model (KP) of semiflexible polymers. Our solution to the model is based on the definition of a generating function which we use to study the statistical mechanics of semiflexible polymer chains. Specifically, we derive mathematical expressions for the characteristic function, the polymer propagator and the mean square end-to-end distance from the generating function. These expressions are valid for polymers with any number of segments and degree of rigidity. Furthermore, they capture the limits of fully flexible and stiff polymers exactly. In between, a smooth and approximate crossover behavior is predicted. The most important contribution of this paper is the expression of the polymer propagator which is written in a very simple and insightful way. It is given in terms of the exact polymer propagator of the Random Flight Model multiplied by an exponential that takes into account the stiffness of the polymer backbone.

Research paper thumbnail of Statistics of Semiflexible Polymer Chains and the Generalized Borel Transform

arXiv (Cornell University), Jun 30, 2003

In this paper, we present a new approach to the discrete version of the Wormlike Chain Model (WCM... more In this paper, we present a new approach to the discrete version of the Wormlike Chain Model (WCM) of semiflexible polymers. Our solution to the model is based on a new computational technique called the Generalized Borel Transform (GBT) which we use to study the statistical mechanics of semiflexible polymer chains. Specifically, we evaluate the characteristic function of the model approximately. Afterward, we compute the polymer propagator of the model using the GBT and find an expression valid for polymers with any number of segments and values of the semiflexibility parameter. This expression captures the limits of flexible and infinitely stiff polymers exactly. In between, a smooth and approximate crossover behavior is predicted. Another property of our propagator is that it fulfills the condition of finite extensibility of the polymer chain. We have also calculated the single chain structure factor. This property is a decreasing function of the wave vector, k,k,k, until a plateau is reached. Our computations clearly show that the structure factor decreases faster with increasing wave vector when the semiflexibility parameter is increased. Furthermore, when the wave vector is large enough, there is a regime where the structure factor follows an approximate power law of the form k−thetak^{-\theta}k−theta even for short polymer chains. theta\thetatheta is equal to two for flexible polymers and to one for rigid chains. We also compare our results to the predictions of other models.

Research paper thumbnail of Electrical impulse characterization along actin filaments in pathological conditions

bioRxiv (Cold Spring Harbor Laboratory), Sep 6, 2021

Research paper thumbnail of A Multi-Scale Approach to Describe Electrical Impulses Propagating along Actin Filaments in both Intracellular and In-vitro Conditions

arXiv (Cornell University), Jan 18, 2018

Research paper thumbnail of Simulations of RNA Interactions with Monovalent Ions

Methods in Enzymology, 2009

RNA folding and binding reactions are mediated by interactions with ions that make up the surroun... more RNA folding and binding reactions are mediated by interactions with ions that make up the surrounding aqueous electrolytic milieu. Although Mg(2+) ions are often implicated as being crucial for RNA folding, it is known that folding is feasible in high concentrations of monovalent alkali-halide salts. Experiments have yielded important information regarding the salt dependence of RNA stability. Recent work has shown that molecular simulations based on explicit representations of solvent molecules and monovalent ions can also provide useful insights regarding the ionic atmospheres around model RNA systems. These insights can help rationalize intriguing observations regarding the dependence of RNA stability on cation type providing one pays attention to important considerations that go into the proper design of molecular simulations. These issues are discussed in detail and the methods are applied to an A-form RNA and B-form DNA sequence. The results of these simulations are compared to previous work on a kissing-loop system with analogous sequence. In particular, ionic atmospheres obtained from molecular simulations are compared to those obtained using the nonlinear Poisson Boltzmann model for continuum electrostatics for these three different nucleic acid systems. The comparisons indicate reasonable agreement in terms of coarse-grained observables such as the numbers of counterions accumulated around the solutes. However, details of the ionic atmospheres, captured in terms of spatial free energy density profiles, are quite different between the two approaches. These comparisons suggest the need for improvements in continuum models to capture sequence-specific effects, ion-ion correlation, and the effects of partial dehydration of ions.

Research paper thumbnail of The Self-Adaptation Ability of Zinc Oxide Nanoparticles Enables Reliable Cancer Treatments

Nanomaterials, Feb 5, 2020

Research paper thumbnail of Suitability of the Method Of Lines for rendering analytic/numeric solutions of the unsteady heat conduction equation in a large plane wall with asymmetric convective boundary conditions

International Journal of Heat and Mass Transfer, Aug 1, 2016

Abstract The primary objective of the present study is to implement the Method Of Lines (MOL) for... more Abstract The primary objective of the present study is to implement the Method Of Lines (MOL) for the analysis of the unsteady, one-dimensional, heat conduction equation in a large plane wall with different convective boundary conditions at the two exposed surfaces. In the equation, MOL discretizes the space derivative while leaving the time derivative continuous. By way of MOL, the adjoint system of linear, first order ordinary differential equations will be solved analytically (not numerically) with the eigenvalue method. The outcome of the computational procedure provides a discrete sequence of piecewise temperatures-time variations at each line, which is expressed in terms of linear combinations of exponential functions of time containing the eigenvalues and eigenvectors. A practical example dealing with the temperature evolution in a large single-pane window is tackled with two meshes, one having three and the other having five lines. The collection of analytic/numeric temperature–time solutions provided by MOL and the eigenvalue method exhibits excellent quality at all time.