Jorge Ramı́rez
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View article: Compression-Induced Communication-Efficient Large Model Training and Inferencing
Compression-Induced Communication-Efficient Large Model Training and Inferencing Open
Energy efficiency of training and inferencing with large neural network models is a critical challenge facing the future of sustainable large-scale machine learning workloads. This paper introduces an alternative strategy, called phantom p…
View article: Chemically Informed Coarse-Graining of Electrostatic Forces in Charge-Rich Biomolecular Condensates
Chemically Informed Coarse-Graining of Electrostatic Forces in Charge-Rich Biomolecular Condensates Open
Biomolecular condensates composed of highly charged biomolecules, such as DNA, RNA, chromatin, and nucleic-acid binding proteins, are ubiquitous in the cell nucleus. The biophysical properties of these charge-rich condensates are largely r…
View article: Computational study of active polar polymer melts: from active reptation to activity induced local alignment
Computational study of active polar polymer melts: from active reptation to activity induced local alignment Open
This work investigates the effects of tangent polar activity on the conformational and dynamic properties of entangled polymer melts through Langevin molecular dynamics simulations. We examine systems composed of all self-propelled, monodi…
View article: Chemically-informed coarse-graining of electrostatic forces in charge-rich biomolecular condensates
Chemically-informed coarse-graining of electrostatic forces in charge-rich biomolecular condensates Open
Biomolecular condensates composed of highly charged biomolecules like DNA, RNA, chromatin, and nucleic-acid binding proteins are ubiquitous in the cell nucleus. The biophysical properties of these charge-rich condensates are largely regula…
View article: Optical Halo: A Proof of Concept for a New Broadband Microrheology Tool
Optical Halo: A Proof of Concept for a New Broadband Microrheology Tool Open
Microrheology, the study of material flow at micron scales, has advanced significantly since Robert Brown’s discovery of Brownian motion in 1827. Mason and Weitz’s seminal work in 1995 established the foundation for microrheology technique…
View article: Progressive polymer deformation induced by polar activity and the influence of inertia
Progressive polymer deformation induced by polar activity and the influence of inertia Open
Polar activity is shown here to induce a progressive local deformation of linear polymer chains, making a clear distinction between head and tail, while the overall chain conformation gets more compact. This breakdown of self-similarity, p…
View article: A Dynamic Likelihood Approach to Filtering for Advection-Diffusion Dynamics
A Dynamic Likelihood Approach to Filtering for Advection-Diffusion Dynamics Open
A Bayesian data assimilation scheme is formulated for advection-dominated advective and diffusive evolutionary problems, based upon the Dynamic Likelihood (DLF) approach to filtering. The DLF was developed specifically for hyperbolic probl…
View article: Progressive polymer deformation induced by polar activity and the influence of inertia
Progressive polymer deformation induced by polar activity and the influence of inertia Open
Polar activity is shown here to induce a progressive local deformation of linear polymer chains, making a clear distinction between head and tail, while the overall chain conformation gets more compact. This breakdown of self-similarity, p…
View article: Effect of substrate mismatch, orientation, and flexibility on heterogeneous ice nucleation
Effect of substrate mismatch, orientation, and flexibility on heterogeneous ice nucleation Open
Heterogeneous nucleation is the main path to ice formation on Earth. The ice nucleating ability of a certain substrate is mainly determined by both molecular interactions and the structural mismatch between the ice and the substrate lattic…
View article: Mold: a LAMMPS package to compute interfacial freeenergies and nucleation rates
Mold: a LAMMPS package to compute interfacial freeenergies and nucleation rates Open
The determination of the free energy cost of forming an interface between two phases, i.e. the interfacial free energy, is critical for characterizing a phase transition.In the particular case of liquid-to-solid transitions, it is not stra…
View article: Labile assembly of a tardigrade protein induces biostasis
Labile assembly of a tardigrade protein induces biostasis Open
Tardigrades are microscopic animals that survive desiccation by inducing biostasis. To survive drying tardigrades rely on intrinsically disordered CAHS proteins, which also function to prevent perturbations induced by drying in vitro and i…
View article: Labile assembly of a tardigrade protein induces biostasis
Labile assembly of a tardigrade protein induces biostasis Open
Tardigrades are microscopic animals that survive desiccation by inducing biostasis. To survive drying tardigrades rely on intrinsically disordered CAHS proteins that form gels. However, the sequence features and mechanisms underlying gel f…
View article: Machine learning opens a doorway for microrheology with optical tweezers in living systems
Machine learning opens a doorway for microrheology with optical tweezers in living systems Open
It has been argued that linear microrheology with optical tweezers (MOT) of living systems “is not an option” because of the wide gap between the observation time required to collect statistically valid data and the mutational times of the…
View article: Location and Concentration of Aromatic‐Rich Segments Dictates the Percolating Inter‐Molecular Network and Viscoelastic Properties of Ageing Condensates
Location and Concentration of Aromatic‐Rich Segments Dictates the Percolating Inter‐Molecular Network and Viscoelastic Properties of Ageing Condensates Open
Maturation of functional liquid‐like biomolecular condensates into solid‐like aggregates has been linked to the onset of several neurodegenerative disorders. Low‐complexity aromatic‐rich kinked segments (LARKS) contained in numerous RNA‐bi…
View article: Time-Dependent Material Properties of Aging Biomolecular Condensates from Different Viscoelasticity Measurements in Molecular Dynamics Simulations
Time-Dependent Material Properties of Aging Biomolecular Condensates from Different Viscoelasticity Measurements in Molecular Dynamics Simulations Open
Biomolecular condensates are important contributors to the internal organization of the cell material. While initially described as liquid-like droplets, the term biomolecular condensates is now used to describe a diversity of condensed ph…
View article: Location and concentration of aromatic-rich segments dictates the percolating inter-molecular network and viscoelastic properties of ageing condensates
Location and concentration of aromatic-rich segments dictates the percolating inter-molecular network and viscoelastic properties of ageing condensates Open
Maturation of functional liquid-like biomolecular condensates into solid-like aggregates has been linked to the onset of several neurodegenerative disorders. Low-complexity aromatic-rich kinked segments (LARKS) contained in numerous RNA-bi…
View article: Time-dependent material properties of ageing biomolecular condensates from different viscoelasticity measurements in molecular dynamics simulations
Time-dependent material properties of ageing biomolecular condensates from different viscoelasticity measurements in molecular dynamics simulations Open
Biomolecular condensates are important contributors to the internal organization of the cell material. While initially described as liquid-like droplets, the term biomolecular condensates is now used to describe a diversity of condensed ph…
View article: Molecular dynamics simulations of active entangled polymers reptating through a passive mesh
Molecular dynamics simulations of active entangled polymers reptating through a passive mesh Open
In this work, we explore the dynamics of active entangled chains using molecular dynamics simulations of a modified Kremer-Grest model. The active chains are diluted in a mesh of very long passive linear chains, to avoid constraint release…
View article: Protein structural transitions critically transform the network connectivity and viscoelasticity of RNA-binding protein condensates but RNA can prevent it
Protein structural transitions critically transform the network connectivity and viscoelasticity of RNA-binding protein condensates but RNA can prevent it Open
Biomolecular condensates, some of which are liquid-like during health, can age over time becoming gel-like pathological systems. One potential source of loss of liquid-like properties during ageing of RNA-binding protein condensates is the…
View article: Homogeneous ice nucleation rates for mW and TIP4P/ICE models through Lattice Mold calculations
Homogeneous ice nucleation rates for mW and TIP4P/ICE models through Lattice Mold calculations Open
Water freezing is the most common liquid-to-crystal phase transition on Earth, however, despite its critical implications on climate change and cryopreservation among other disciplines, its characterization through experimental and computa…
View article: Homogeneous ice nucleation rates for mW and TIP4P/ICE models through Lattice Mold calculations
Homogeneous ice nucleation rates for mW and TIP4P/ICE models through Lattice Mold calculations Open
Freezing of water is the most common liquid-to-crystal phase transition on Earth; however, despite its critical implications on climate change and cryopreservation among other disciplines, its characterization through experimental and comp…
View article: Homogeneous ice nucleation rates for mW and TIP4P/ICE models through Lattice Mold calculations
Homogeneous ice nucleation rates for mW and TIP4P/ICE models through Lattice Mold calculations Open
Water freezing is the most common liquid-to-crystal phase transition on Earth, however, despite its critical implications on climate change and cryopreservation among other disciplines, its characterization through experimental and computa…
View article: Dynamical anomalies and structural features of active Brownian particles characterized by two repulsive length scales
Dynamical anomalies and structural features of active Brownian particles characterized by two repulsive length scales Open
In this work, we study a two-dimensional system composed by Active Brownian Particles (ABPs) interacting via a repulsive potential with two length scales—a soft shell and a hard core. Depending on the ratio between the strength of the soft…
View article: Protein structural transitions critically transform the network connectivity and viscoelasticity of RNA-binding protein condensates but RNA can prevent it
Protein structural transitions critically transform the network connectivity and viscoelasticity of RNA-binding protein condensates but RNA can prevent it Open
Biomolecular condensates, some of which are liquid-like during health, can age over time becoming gel-like pathological systems. One potential source of loss of liquid-like properties during ageing of RNA-binding protein condensates is the…
View article: Dynamical anomalies and structural features of Active Brownian Particles characterised by two repulsive length scales
Dynamical anomalies and structural features of Active Brownian Particles characterised by two repulsive length scales Open
In this work we study a two-dimensional system composed by Active Brownian Particles (ABPs) interacting via a repulsive potential with two-length-scales, a soft shell and a hard-core. Depending on the ratio between the strength of the soft…