News
Job Announcement: PostDoc Positions
PostDoc position is available in our group to work on "Study of extracellular vesicle fusion via molecular dynamics simulations". Details on:
https://web.uniroma1.it/trasparenza/dettaglio_bando_albo/210106PostDoc position is available in our group to work on "Numerical simulations of nanoporous materials for the creation of advanced vibration dampers for applications advanced engineering and aerospace". Details on:
https://web.uniroma1.it/trasparenza/dettaglio_bando_albo/210092
Summer workshop: "From biology to bioinspiration: theory, simulation, and experiments for biophysical systems"
June 20-23 2022 - Poreta, Italy
Understanding the behavior of biological systems, in addition to being relevant per se, is an endless source of inspiration for the design of new materials and nanoscale devices. Molecular simulations can reveal mechanistic insights into important biological processes occurring at the cellular membrane, such as transport of ions and particles, but face important methodological challenges due to their multiscale nature. This workshop is aimed at exchanging cutting-edge ideas concerning soft matter systems, ranging from modeling and simulation to the experimental study of real biological and bio-inspired systems. Specifically, the workshop will focus on three main topics: Functionalized Nanoparticles, Peptides, and Biological Nanopores. From a methodological point of view, dedicated Rare Event and Machine Learning strategies will be discussed as a means to empower atomistic simulations of soft biological systems.
External guests: P. Bergese, C.M. Casciola, M. Chinappi, M. Cretich, G. Maglia, L. Maragliano, E. Milanetti, G. Rossi, G. Tribello
ERC Proof of Concept awarded to the group for Project NODRY
Project NODRY - Designing green and energy-efficient anti-dewetting protocols for liquid chromatography
7 February 2022
High Performance Liquid Chromatography (HPLC) is the leading separation technology in research and industry, which often relies on potentially hazardous and environmentally harmful organic solvents. Water is the ideal environmentally friendly mobile phase, which would open the way to green HPLC. However, its broad applicability is hindered by the phenomenon of dewetting of the stationary phase – the formation of bubbles in the hydrophobic nanoporous material – which makes it unavailable to the substances that need to be separated (“retention loss”). NODRY proposes to develop a unique, experimentally validated simulation testbed based on the PI expertise in theory and simulation of dewetting of nanopores acquired in ERC-StG HyGate. These simulation tools will be deployed to rationally design HPLC protocols capable of eliminating or alleviating the problem of dewetting in most HPLC columns operating with pure water as the solvent, thus opening the way to a green and energy efficient chromatography.
https://erc.europa.eu/news/erc-2021-proof-of-concept-grants-results
Seminar of Prof. Guido Raos on "Polymer adhesion: fundamentals and molecular simulations"
19 January 2022 h 11.00 - https://meet.google.com/whq-nqsr-cwk
Incontri e seminari - Facoltà di Ingegneria Civile e Industriale
INgegneria INcontra Alberto Giacomello
Nanobiomimetica: imparare dalla natura a manovrare singole molecole
La nostra vita dipende dalla capacità di movimentare singole molecole dentro o fuori dalle cellule. Negli esseri viventi, congegni molecolari sovrintendono a queste operazioni fondamentali in maniera robusta e con precisione atomica. Un esempio di straordinaria importanza è la trasmissione di informazione nel nostro sistema nervoso, che avviene controllando il flusso di ioni attraverso la membrana cellulare. I canali ionici sono i “nanointerruttori” che consentono il passaggio di un solo tipo di ioni nelle cellule e ne possono interrompere il flusso. I più recenti strumenti della biologia consentono oggi di conoscere la struttura di tali proteine, di sostituire singoli atomi e di misurare le correnti ioniche di un singolo canale. Cosa può l’ingegneria imparare da queste straordinarie nanostrutture e dai recenti avanzamenti in biologia? Ma soprattutto, come può un approccio ingegneristico ai problemi biologici ispirare tecnologie radicalmente nuove?
https://www.ing.uniroma1.it/sites/default/files/inin/Videoconferenza_Giacomello2021.mp4
Seminar of Prof. Matteo Masetti on "Enhanced MD simulations in computational drug discovery"
16 July 2021 h 10.30 - Room 7, Department of Mechanical and Aerospace Engineering
Bringing a new drug to market is a resource-intensive and time-consuming activity characterized by a high rate of failure. Computational methods can assist the entire process in many ways, and they are nowadays considered an integral part of any modern drug discovery and development program. Thanks to recent progress in hardware performances, Molecular Dynamics (MD) simulations and related methods have gained mainstream status in the field of computational medicinal chemistry, as in principle they allow predicting drug-target binding modes, binding free energies, and kinetic rate constants. Unfortunately, the computational cost of MD simulations remains prohibitive, and several workarounds (usually referred to as “enhanced sampling”) have been devised to make this kind of computations affordable and therefore appealing from a drug discovery standpoint. One class of such methods is based on the notion of Collective Variables (CV), or reaction coordinates, by which the process of interest can be described and investigated through the introduction of external biases. As a result, rare events can be sampled at a greatly reduced computational cost compared to conventional MD. An adding value of these methods is that the Free Energy Surface (FES) along the chosen CVs is also an outcome of the simulation, providing a mechanistic interpretation of the process under investigation. In this seminar, an introduction to enhanced sampling methods making use of CVs for reconstructing the FES will be addressed. Specifically, the method of metadynamics and its application to pharmaceutically relevant case studies will be discussed. A special emphasis will be given to the importance of choosing suitable CVs for the reliability of the FES, and how trajectories produced by conventional MD simulations can be harnessed to devise optimal CVs in a data-driven fashion.
Summer workshop: "Phase transitions at the nanoscale: wetting of the nanoporous materials, cluster formation, and nanofriction"
June 23-26 2021 - S. Anna in Camprena, Italy
Phase transitions occurring in nanoscale systems or in nanoconfinement may have a dramatic influence on the macroscopic behavior of physical systems, calling for a truly multiscale understanding of such phenomena. These kinds of systems are ubiquitous in nature and technology and have intriguing properties such as superhydrophobicity, rate dependent wetting, and superlubricity. Hence, the study of phase transitions at the nanoscale is of great importance for understanding the behavior of such heterogeneous systems and to exploit their properties for the design of new devices. This workshop is aimed at exchanging cutting-edge ideas concerning phase transitions at the nanoscale, ranging from modeling and simulation to the experimental study of real systems. Specifically, the workshop will focus on three main topics: the wetting of nanoporous materials and their energy absorption properties, the formation of nanoclusters and nanoalloys, and the friction of materials at the nanoscale. The workshop will be held in the fascinating venue of the ancient monastery of Sant’Anna in Camprena, in Tuscany.
External guests: B. Coasne, R. Ferrando, N. Manini, C.M. Casciola, Y. Grosu, S. Meloni.
Proud to announce the new computational cluster co-funded by ERC and Sapienza University of Rome.
"Monolith" will give momentum to the computational research of the nanoCAFÉ group!
April 30 2021 - Rome
Workshop: "Frontiers in ion channels and nanopores: theory, experiments and simulation"
February 2-5 2021 - Rome
Ion channels are fundamental biological devices that act as gates in order to ensure selective ion transport across cellular membranes; their operation constitutes the molecular mechanism through which basic biological functions, such as nerve signal transmission and muscle contraction, are carried out. Nowadays biological nanopores can be inserted in lipid bilayers and reproducibly prepared allowing several applications in nanobiotechnology such as single molecule detection and manipulation. The power of these tools is exemplified by the ultra-fast DNA sequencing technique based on the alpha-hemolysine channel. Ion channels are, however, extremely sensitive to the external environment and once they are extracted from their biological setting, they tend to lose their unique properties. This has prompted massive research efforts in order to produce synthetic nanopores in solid-state materials; these artificial nanopores, however, still do not fully replicate the properties of ion channels. Indeed, a number of stimulating challenges are ahead, such as combining the exquisite selectivity of biological pores with the robustness of synthetic ones. From a more general perspective the study of biological ion channels enshrines the possibility to identify the design principles for biomimetic nanopores, and as such it is of great interest not only for the biophysical, but also for the nanotech community. This workshop brings together leading and emerging scientists in the field of ion channels and nanopores covering theoretical advances, state-of-the-art simulation approaches, and frontline experimental techniques. The speakers are selected among renowned experimentalists, theoreticians, simulators and technologists. The informal atmosphere is intended to promote the interaction of young researchers with leading scientists.
External guests: G. Hummer, M. Sansom, S. Sukharev, S. Meloni, B. Roux, C. Schütte, E. Vanden-Eijnden, B. Corry, L. Delemotte, M. Grabe, W. Treptow, M. Ceccarelli, F. Bezanilla, A. Moroni, C. Nimigean, M. Prakriya, G. Thiel, A. Kocer, A. Radenovic, A. Siria, M. Mayer, Y. Grosu, R. Remsing, R. Roth.
Summer workshop: "Multiscale simulations and biological channels"
September 13-16 2020 - Rocca Calascio, Italy
Recently developed computational methods allow the simulation of systems in which different parts are treated at different levels of resolution, ranging from quantum to atomistic and coarse-grained descriptions. Such multiscale simulations promise to have a disruptive impact in the computational study of complex biological systems as biological channels. Biological channels are expressed by all living cells; these proteins allow ion movements across the hydrophobic membranes playing an important role in many physiological processes, e.g., nerve or muscle excitation. This is possible by different gating mechanisms which modulate the transition between the open and closed states of the channels. A non-canonical gating mechanism is the hydrophobic gating which originates from the reversible formation of a vapor bubble in the extremely confined inner pore region of channels. The quantification of hydrophobic gating in ion channels requires the use of computational methods able to simulate the broad range of spatial and temporal scales involved. This workshop is aimed at exchanging cutting-edge ideas concerning biological nanochannels and their gating mechanisms, with a specific focus on hydrophobic gating and on the enabling multiscale simulations.
External guests: G. Camisasca, C.M. Casciola, R. Cortes-Huerto, B. de Groot, G. Maglia, S. Meloni.
Seminar of Prof. Luigi Catacuzzeno on "Patch-Clamp single channel recording as a tool for dissecting kinetically distinct gating states in ion channels"
November, 8 2019
Using the patchclamp technique, electrophysiologists have been able to record the ionic fluxes through the pore of single channel proteins, and to clearly distinguish when the channel is functionally closed and when it is open. The detailed analysis of these recordings, namely the resulting open and closed dwell time histograms, has shown the existence of a large number of energetically distinct conformational states, whose behavior and connectivity could be well interpreted using discrete Markov models and transition state theory. These studies indicated that ion channels typically have relatively few open states but many closed states. More recently, the availability of three-dimensional crystallographic structures of ion channels that provide essential clues on the physical determinants of channels conformational transitions and conformational states, and mutagenesis experiments performed under conditions capable to modulate channel gating, suggested the presence of two gating structures and mechanisms: an intracellular channel domain that undergoes conformational transitions resulting in the opening and closing of the permeation pore; a second conformational transition observed to occur more extracellularly, in the selectivity filter of the channel, and to underlie a second form of gating, which likewise resulted in the opening and closing of the channel pore. Notably, the number of conformational states normally identified in channel gating from crystallographic structures/mutagenesis experiments are largely fewer than the number of energetically distinct conformational states suggested by discrete Markov models. This observation raises the possibility that not all forms of gating originate from conformational transitions of the channel protein.
Seminar of Prof. Bob Eisenberg on "Biological channels as natural templates for nanodevices"
November, 4 2019
Biological channels are well defined devices with robust input output relations determined by: I) Gating: the on-off behavior of single channel proteins; II) Permeation: what goes through the narrow pore once it is open; III) Controls of gating: separate nanosensors that detect chemicals, voltage, stretch, etc., by controlling the parameters of single channel gating. These properties are not automatic physical properties of narrow channels. Rather evolution has chosen a combination of permanent charge density (from specific chemical properties of acid and base side chains of proteins); polarization charge (crudely described by local dielectric constant); shape of the pore; (perhaps) changes of the shape of the pore. Physical scientists might follow evolution by choosing properties of nanosensors that produce useful robust device equations.
Seminar of Prof. Chiara Neto on "Drag reduction and boundary slip at silicone oil-water interfaces"
October, 9 2019
The Nepenthes pitcher plant has structured surfaces that are designed to trap a thin lubricating layer of water, which makes then slippery and helps in the capture of insects. There is recent evidence that artificial lubricant-infused surfaces can reduce drag in turbulent and laminar flow. Here, the flow of aqueous solutions of various viscosities over silicon oil-infused nanostructured surfaces was investigated in microfluidic devices. The measured pressure drop across a channel is lower than that expected for a no-slip boundary condition, and the measured drag reduction is as high as 28 %, corresponding to a slip length of 16 micrometers. The results cannot be explained with the existing theory, but are consistent with slip occurring at the liquid-liquid interface.