Salvatore Assenza

Salvatore Assenza
Universidad Autónoma de Madrid | UAM · Departamento de Física Teórica de la Materia Condensada

PhD Physics, EPFL

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29
Publications
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576
Citations

Publications

Publications (29)
Article
Full-text available
We introduce MADna, a sequence-dependent coarse-grained model of double-stranded DNA (dsDNA), where each nucleotide is described by three beads localized at the sugar, at the base moiety, and at the phosphate group, respectively. The sequence dependence is included by considering a step-dependent parametrization of the bonded interactions, which ar...
Preprint
A detailed understanding of the mechanism by which Hsp70 chaperones protect cells against protein aggregation is hampered by the detailed characterization of the aggregates, which are typically heterogeneous. To tackle this problem, we designed here a reporter chaperone substrate, MLucV, composed of a stress-labile luciferase core, flanked by stres...
Preprint
Full-text available
We introduce MADna, a sequence-dependent coarse-grained model of double-stranded DNA (dsDNA), where each nucleotide is described by three beads localized at the sugar and base moieties, and at the phosphate group. The sequence dependence is included by considering a step-dependent parameterization of the bonded interactions, which are tuned in orde...
Article
Colloidal lipidic particles with different space groups and geometries (mesosomes) are employed in the development of new nanosystems for the oral delivery of drugs and nutrients. Understanding of the enzymatic digestion rate of these particles is key to the development of novel formulations. In this work, the molecular structure of the lipids has...
Article
The fine interplay between the simultaneous stretching and confinement of amyloid fibrils is probed by combining a microcapillary setup with atomic force microscopy. Single-molecule statistics reveal how the stretching of fibrils changed from force to confinement dominated at different length scales. System order, however, is solely ruled by confin...
Article
Full-text available
Hsp70 molecular chaperones are abundant ATP-dependent nanomachines that actively reshape non-native, misfolded proteins and assist a wide variety of essential cellular processes. Here we combine complementary theoretical approaches to elucidate the structural and thermodynamic details of the chaperone-induced expansion of a substrate protein, with...
Article
Full-text available
Chiral liquid crystals, or cholesteric phases, have been widely studied in the last decades, leading to fundamental advances and a multitude of applications and technologies. In general, the rich phenomenology of these systems depends directly on the molecular traits and conditions of the system, imposing precise symmetry to the resulting nematic f...
Article
This Review tackles how soft condensed matter physics can assist in the understanding of complex food systems, by relying on the foundations of established theories on polymers, colloids and surfactants to unravel the properties of food macrocomponents and the challenges associated with this task.
Article
Full-text available
Water is a ubiquitous liquid with unique physicochemical properties, whose nature has shaped our planet and life as we know it. Water in restricted geometries has different properties than in bulk. Confinement can prevent low-temperature crystallization of the molecules into a hexagonal structure and thus create a state of amorphous water. To under...
Article
Water nanoconfinement has important effects on the properties of biomolecules and ultimately on their specific functions. By performing experiments and molecular dynamic simulations, in this work we show how intrinsic nanoconfinement controls the crystallization of small organic molecules converted by enzymatic reactions within the water nanochanne...
Article
Water nanoconfinement has important effects on the properties of biomolecules and ultimately on their specific functions. By performing experiments and molecular dynamic simulations, in this work we show how intrinsic nanoconfinement controls the crystallization of small organic molecules converted by enzymatic reactions within the water nanochanne...
Article
The present work addresses the effect of partial equilibration and molecular partitioning on the interpretation of release experiments. In this regard, it is shown how release profiles and the values of extracted transport parameters are affected by the time protocol chosen for sample collection by considering a series of experiments where the latt...
Article
Full-text available
The transport behavior of inverse bicontinuous cubic phases is experimentally investigated as the combined outcome of solute molecular structure and geometrical details of the confining symmetry. Molecular diffusion is discussed in relation to curvature, bottlenecks, and interfacial properties of each cubic phase. Point-like molecules show faster d...
Preprint
Hsp70 molecular chaperones are abundant ATP-dependent nanomachines that actively reshape non-native, misfolded proteins and assist a wide variety of essential cellular processes. Here we combine complementary computational/theoretical approaches to elucidate the structural and thermodynamic details of the chaperone-induced expansion of a substrate...
Article
Full-text available
Cellulose is a pervasive polymer, displaying hierarchical lengthscales and exceptional strength and stiffness. Cellulose's complex organization, however, also hinders the detailed understanding of the assembly, mesoscopic properties, and structure of individual cellulose building blocks. This study combines nanolithography with atomic force microsc...
Preprint
Water is a ubiquitous liquid with unique physico-chemical properties, whose nature has shaped our planet and life as we know it. Water in restricted geometries has different properties than in bulk. Confinement can prevent low-temperature crystallization into a hexagonal structure, thus creating a state of amorphous water. In this work we introduce...
Article
Full-text available
Class-I aldolases are known for efficiently catalysing stereo-selective aldol-addition reactions in bulk aqueous media and considerable efforts are currently being devoted to engineer the enzyme in order to optimize its activity and stability, primarily by modulating the hydrophobicity of the catalytic active site. Here, we opt for a different stra...
Article
We perform a simulation study of the diffusion of small solutes in the confined domains imposed by inverse bicontinuous cubic phases for the primitive, diamond, and gyroid symmetries common to many lipid/water mesophase systems employed in experiments. For large diffusing domains, the long-time diffusion coefficient shows universal features when th...
Article
We present an experimental investigation on the diffusion of unfolded polymers in the triply-periodic water-channel network of inverse bicontinuous cubic phases. Depending on the chain size, our results indicate the presence of two different dynamical regimes corresponding to Zimm and Rouse diffusion. We support our findings by scaling arguments ba...
Article
Lyotropic Liquid Crystals (LLCs) are a class of lipid-based membranes with a strong potential for drug-delivery employment. The characterization and control of their transport properties is a central issue in this regard, and has recently prompted a notable volume of research on the topic. A promising experimental approach is provided by the so-cal...
Article
The shape of a polymer plays an important role in determining its interactions with other molecules and with the environment, and is in turn affected by both of them. As a consequence, in the literature the shape properties of a chain in many different conditions have been investigated. Here, we characterize the shape and orientational properties o...
Article
Boosted by the technological advances in experimental techniques, cellular biology is nowadays facing the need for quantitative approaches in order to rationalize the huge amount of collected data. A particularly succesfull theoretical framework is provided by Polymer Theory which, combined with molecular simulations, can capture the essential feat...
Article
Amyloid fibrils are ubiquitous proteinaceous aggregates occurring in vivo and in vitro, with an invariant structural fingerprint at the molecular length scale. However, interpretation of their mesoscopic architectures is complicated by diverse observable polymorphic states. We here present a constitutive model for amyloid fibrils based on the minim...
Article
Full-text available
The molecular chaperone Hsp70 plays a central role in the import of cytoplasmic proteins into organelles, driving their translocation by binding them from the organellar interior. Starting from the experimentally-determined structure of the \textit{E. coli} Hsp70, we computed, by means of molecular simulations, the effective free-energy profile for...
Article
We consider a set of interacting phase oscillators, with a coupling between synchronized nodes adaptively reinforced, and the constraint of a limited resource for a node to establish connections with the other units of the network. We show that such a competitive mechanism leads to the emergence of a rich modular structure underlying cluster synchr...
Article
Full-text available
Synchronization is a collective phenomenon occurring in systems of interacting units, and is ubiquitous in nature, society and technology. Recent studies have enlightened the important role played by the interaction topology on the emergence of synchronized states. However, most of these studies neglect that real world systems change their interact...
Article
Full-text available
We study the effect of clustering on the organization of cooperation by analyzing the evolutionary dynamics of the "Prisoner's Dilemma" on scale-free networks with a tunable value of clustering. We find, on the one hand, that a high value of the clustering coefficient produces an overall enhancement of cooperation in the network, even for a very hi...

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