arXiv subjects

Matej Praprotnik

Publications and source records attributed to Matej Praprotnik.

17 recordsLinked to original sources

arXiv2026

Hierarchical Bayesian calibration of mesoscopic models for ultrasound contrast agents from force spectroscopy data

Ultrasound-guided drug and gene delivery (USDG) is a promising non-invasive approach for targeted therapeutic applications. Mechanical properties of encapsulated microbubbles (EMBs), which serve as contrast agents, strongly affect their specific interactions with ultrasound and are thus critical to the success and efficiency of USDG. Accurate calibration of high-fidelity particle-based models of EMB capsid mechanics is computationally challenging because direct Bayesian inference with dissipative particle dynamics (DPD) is prohibitively expensive. We employ a surrogate-accelerated Bayesian calibration workflow that combines deep neural network (DNN) surrogates, transitional Markov chain Monte Carlo sampling, and hierarchical regularization across EMB diameters. Using this framework, we develop two data-informed DPD models of commercial EMB agents, i.e., Definity and SonoVue, and perform inference of force field parameters based on published compression experiments for Definity and indentation experiments for SonoVue, each spanning three distinct diameters. The inferred posteriors show that key model parameters, such as the stretching stiffness and bending modulus, are consistently constrained by the available data. The presented methodology can be used to derive bespoke, data-informed models for a wide range of ultrasound contrast agents, including encapsulated gas vesicles, EMBs with diverse capsids consisting of lipids, proteins, or polymers, and functionalized with ligands.

cond-mat.soft↗

arXiv2026

Virtual ultrasound machine operating in a GHz to MHz frequency range for particle-based biomedical simulations

Ultrasound-matter interactions underpin numerous biomedical and soft-matter applications, yet simulating these phenomena is challenging due to the large separation of viscous and sonic time scales. Continuum methods capture large-scale wave propagation but cannot resolve microscale interactions, while particle-based approaches offer molecular resolution but struggle with efficiency and stability at larger scales. We introduce a particle-based virtual ultrasound machine that uses a novel smoothed dissipative particle dynamics variant with an implicit pressure solver and a negative-pressure stabilization scheme, required to mimic acoustic propagation across MHz-GHz frequencies. We demonstrate its capabilities by modeling the acoustophoresis of encapsulated microbubbles, a key mechanism in ultrasound-mediated drug delivery. Beyond this application, the approach establishes a generalizable platform for simulating wave-matter interactions in soft and biological materials, opening new directions for computational studies of acoustics-driven phenomena in science and engineering.

cond-mat.soft↗

arXiv2025

Dissipative particle dynamics models of encapsulated microbubbles and gas vesicles for biomedical ultrasound simulations

Ultrasound-guided drug and gene delivery (usdg) enables controlled and spatially precise delivery of drugs and macromolecules, encapsulated in microbubbles (embs) and submicron gas vesicles (gvs), to target areas such as cancer tumors. It is a non-invasive, high precision, low toxicity process with drastically reduced drug dosage. Rheological and acoustic properties of gvs and embs critically affect the outcome of usdg and imaging. Detailed understanding and modeling of their physical properties is thus essential for ultrasound-mediated therapeutic applications. State-of-the-art continuuum models of shelled bodies cannot incorporate critical details such as varying thickness of the encapsulating shell or specific interactions between its constituents and interior or exterior solvents. Such modeling approaches also do not allow for detailed modeling of chemical surface functionalizations, which are crucial for tuning the gv-blood interactions. We develop a general particle-based modeling framework for encapsulated bodies that accurately captures elastic and rheological properties of gvs and embs. We use dissipative particle dynamics to model the solvent, the gaseous phase in the capsid, and the triangulated surfaces of immersed objects. Their elastic behavior is studied and validated through stretching and buckling simulations, eigenmode analysis, shear flow simulations, and comparison of predicted gv buckling pressure with experimental data from the literature. The presented modeling approach paves the way for large-scale simulations of encapsulated bodies, capturing their dynamics, interactions, and collective behavior.

cond-mat.soft↗

arXiv2024

The need to implement FAIR principles in biomolecular simulations

This letter illustrates the opinion of the molecular dynamics (MD) community on the need to adopt a new FAIR paradigm for the use of molecular simulations. It highlights the necessity of a collaborative effort to create, establish, and sustain a database that allows findability, accessibility, interoperability, and reusability of molecular dynamics simulation data. Such a development would democratize the field and significantly improve the impact of MD simulations on life science research. This will transform our working paradigm, pushing the field to a new frontier. We invite you to support our initiative at the MDDB community (https://mddbr.eu/community/) Now published as: Amaro, R.E., et al. The need to implement FAIR principles in biomolecular simulations. Nat Methods (2025) https://doi.org/10.1038/s41592-025-02635-0

q-bio.BM↗

arXiv2021

Accelerated Simulations of Molecular Systems through Learning of their Effective Dynamics

Simulations are vital for understanding and predicting the evolution of complex molecular systems. However, despite advances in algorithms and special purpose hardware, accessing the timescales necessary to capture the structural evolution of bio-molecules remains a daunting task. In this work we present a novel framework to advance simulation timescales by up to three orders of magnitude, by learning the effective dynamics (LED) of molecular systems. LED augments the equation-free methodology by employing a probabilistic mapping between coarse and fine scales using mixture density network (MDN) autoencoders and evolves the non-Markovian latent dynamics using long short-term memory MDNs. We demonstrate the effectiveness of LED in the M\"ueller-Brown potential, the Trp Cage protein, and the alanine dipeptide. LED identifies explainable reduced-order representations and can generate, at any instant, the respective all-atom molecular trajectories. We believe that the proposed framework provides a dramatic increase to simulation capabilities and opens new horizons for the effective modeling of complex molecular systems.

physics.comp-ph↗

arXiv2018

Density--nematic coupling in isotropic linear polymers

Linear polymers and other connected "line liquids" exhibit a coupling between density and equilibrium nematic order on the macroscopic level that gives rise to a Meyer-de Gennes vectorial conservation law. Nevertheless, isotropic linear polymer melts/solutions exhibit fluctuations of the density and of the nematic order that are not coupled by this vectorial constraint, just like for isotropic liquids composed of disconnected non-spherical particles. It takes the proper tensorial description of the nematic order in linear polymer liquids, leading to a tensorial conservation law connecting density and orientational order, that finally implicates coupled density and nematic order fluctuations, already in the isotropic system and not subject to the existence of an orientational phase transition. This coupling implies that a spatial variation of density or a local concentration gradient will induce nematic order and thereby an acoustic or osmotic optical birefringence even in an otherwise isotropic polymer melt/solution. We validate the theoretical conceptions by performing detailed Monte Carlo simulations of isotropic melts of "soft" worm-like chains with variable length and flexibility, and comparing the numerically determined orientation correlation functions with predictions of the macroscopic theory. The methodology drawn sets forth a means of determining the macroscopic parameters by microscopic simulations to yield realistic continuum models of specific polymeric materials.

cond-mat.soft↗

arXiv2018

Adaptive Resolution Molecular Dynamics Technique: Down to the Essential

We investigate the role of the thermodynamic (TD) force, as an essential and sufficient technical ingredient for an efficient and accurate adaptive resolution algorithm. Such a force applied in the coupling region of an adaptive resolution Molecular Dynamics (MD) set-up, assures thermodynamic equilibrium between atomistically resolved and coarse-grained regions, allowing the proper exchange of molecules. We numerically prove that indeed for systems as relevant as liquid water and 1,3-dimethylimidazolium chloride ionic liquid, the combined action of the TD force and thermostat allows for computationally efficient and numerically accurate simulations, beyond the current capabilities of adaptive resolution set-ups, which employ switching functions in the coupling region.

physics.comp-ph↗

arXiv2018

Splay--density coupling in semiflexible main-chain nematic polymers with hairpins

We establish a macroscopic description of the splay--density coupling in semiflexible main-chain nematic polymers with hairpins, using a vectorial continuity constraint for the "recovered" polar order of the chain tangents and introducing chain backfolds (hairpins) as its new type of sources besides chain ends. We treat both types of sources on a unified basis as a mixture of two ideal gases with fixed composition. Performing detailed Monte Carlo simulations of nematic monodomain melts of "soft" worm-like chains with variable length and flexibility, we show via their structure factors that the chain backfolding weakens the splay--density coupling, and demonstrate how this weakening can be consistently quantified on the macroscopic level. We also probe and discuss the deviations from the noninteracting gas idealization of the chain ends and backfolds.

cond-mat.soft↗

arXiv2017

Application of the Eckart frame to soft matter: rotation of star polymers under shear flow

The Eckart co-rotating frame is used to analyze the dynamics of star polymers under shear flow, either in melt or solution and with different types of bonds. This formalism is compared with the standard approach used in many previous studies on polymer dynamics, where an apparent angular velocity $\omega$ is obtained from relation between the tensor of inertia and angular momentum. A common mistake is to interpret $\omega$ as the molecular rotation frequency, which is only valid for rigid-body rotation. The Eckart frame, originally formulated to analyze the infrared spectra of small molecules, dissects different kinds of displacements: vibrations without angular momentum, pure rotation, and vibrational angular momentum (leading to a Coriolis cross-term). The Eckart frame co-rotates with the molecule with an angular frequency $\Omega$ obtained from the Eckart condition for minimal coupling between rotation and vibration. The standard and Eckart approaches are compared with a straight description of the star's dynamics taken from the time autocorrelation of the monomers positions moving around the molecule's center of mass. This is an underdamped oscillatory signal, which can be described by a rotation frequency $\omega_R$ and a decorrelation rate $\Gamma$. We consistently find that $\Omega$ coincides with $\omega_R$, which determines the characteristic tank-treading rotation of the star. By contrast, the apparent angular velocity $\omega < \Omega$ does not discern between pure rotation and molecular vibrations. We believe that the Eckart frame will be useful to unveil the dynamics of semiflexible molecules where rotation and deformations are entangled, including tumbling, tank-treading motions and breathing modes.

cond-mat.soft↗

arXiv2009

Coupling different levels of resolution in molecular simulations

Simulation schemes that allow to change molecular representation in a subvolume of the simulation box while preserving the equilibrium with the surrounding introduce conceptual problems of thermodynamic consistency. In this work we present a general scheme based on thermodynamic arguments which ensures thermodynamic equilibrium among the molecules of different representation. The robustness of the algorithm is tested for two examples, namely an adaptive resolution simulation, atomistic/coarse-grained, for a liquid of tetrahedral molecules and an adaptive resolution simulation of a binary mixture of tetrahedral molecules and spherical solutes.

cond-mat.stat-mech↗

arXiv2009

Coupling atomistic and continuum hydrodynamics through a mesoscopic model: application to liquid water

We have conducted a triple-scale simulation of liquid water by concurrently coupling atomistic, mesoscopic, and continuum models of the liquid. The presented triple-scale hydrodynamic solver for molecular liquids enables the insertion of large molecules into the atomistic domain through a mesoscopic region. We show that the triple-scale scheme is robust against the details of the mesoscopic model owing to the conservation of linear momentum by the adaptive resolution forces. Our multiscale approach is designed for molecular simulations of open domains with relatively large molecules, either in the grand canonical ensemble or under non-equilibrium conditions.

cond-mat.soft↗

arXiv2007

Modeling Diffusive Dynamics in Adaptive Resolution Simulation of Liquid Water

We present a dual-resolution molecular dynamics (MD) simulation of liquid water employing a recently introduced Adaptive Resolution Scheme (AdResS). The spatially adaptive molecular resolution procedure allows for changing from a coarse-grained to an all-atom representation and vice-versa on-the-fly. In order to find the most appropriate coarse-grained water model to be employed with AdResS we first study the accuracy of different coarse-grained water models in reproducing the structural properties of the all-atom system. Typically, coarse-grained molecular models have a higher diffusion constant than the corresponding all-atom models due to the reduction in degrees of freedom (DOFs) upon coarse-graining that eliminates the fluctuating forces associated with those integrated-out molecular DOFs. Here, we introduce the methodology to obtain the same diffusional dynamics across different resolutions. We show that this approach leads to the correct description of essential thermodynamic, structural and dynamical properties of liquid water at ambient conditions.

cond-mat.soft↗

arXiv2007

Transport properties controlled by a thermostat: An extended dissipative particle dynamics thermostat

We introduce a variation of the dissipative particle dynamics (DPD) thermostat that allows for controlling transport properties of molecular fluids. The standard DPD thermostat acts only on a relative velocity along the interatomic axis. Our extension includes the damping of the perpendicular components of the relative velocity, yet keeping the advantages of conserving Galilei invariance and within our error bar also hydrodynamics. This leads to a second friction parameter for tuning the transport properties of the system. Numerical simulations of a simple Lennard-Jones fluid and liquid water demonstrate a very sensitive behaviour of the transport properties, e.g., viscosity, on the strength of the new friction parameter. We envisage that the new thermostat will be very useful for the coarse-grained and adaptive resolution simulations of soft matter, where the diffusion constants and viscosity of the coarse-grained models are typically too high/low, respectively, compared to all-atom simulations.

cond-mat.soft↗

arXiv2007

A Macromolecule in a Solvent: Adaptive Resolution Molecular Dynamics Simulation

We report adaptive resolution molecular dynamics simulations of a flexible linear polymer in solution. The solvent, i.e., a liquid of tetrahedral molecules, is represented within a certain radius from the polymer's center of mass with a high level of detail, while a lower coarse-grained resolution is used for the more distant solvent. The high resolution sphere moves with the polymer and freely exchanges molecules with the low resolution region through a transition regime. The solvent molecules change their resolution and number of degrees of freedom on-the-fly. We show that our approach correctly reproduces the static and dynamic properties of the polymer chain and surrounding solvent.

cond-mat.soft↗

arXiv2006

Adaptive Resolution Simulation of Liquid Water

We present a multiscale simulation of liquid water where a spatially adaptive molecular resolution procedure allows for changing on-the-fly from a coarse-grained to an all-atom representation. We show that this approach leads to the correct description of all essential thermodynamic and structural properties of liquid water.

cond-mat.soft↗

arXiv2006

Adaptive molecular resolution via a continuous change of the phase space dimensionality

For the study of complex synthetic and biological molecular systems by computer simulations one is still restricted to simple model systems or to by far too small time scales. To overcome this problem multiscale techniques are being developed for many applications. However in almost all cases, the regions of different resolution are fixed and not in a true equilibrium with each other. We here give the theoretical framework for an efficient and flexible coupling of the different regimes. The approach leads to an analog of a geometry induced phase transition and a counterpart of the equipartition theorem for fractional degrees of freedom. This provides a rather general formal basis for advanced computer simulation methods applying different levels of resolution.

cond-mat.stat-mech↗

arXiv2005

Adaptive Resolution Molecular Dynamics Simulation: Changing the Degrees of Freedom on the Fly

We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially localized domains whereas a lower mesoscopic level of detail is sufficient for the rest of the system. Our method allows an on-the-fly interchange between a given molecule's atomic and coarse-grained level of description, enabling us to reach large length and time scales while spatially retaining atomistic details of the system. The new approach is tested on a model system of a liquid of tetrahedral molecules. The simulation box is divided into two regions: one containing only atomistically resolved tetrahedral molecules, the other containing only one particle coarse-grained spherical molecules. The molecules can freely move between the two regions while changing their level of resolution accordingly. The coarse-grained and the atomistically resolved systems have the same statistical properties at the same physical conditions.

cond-mat.soft↗