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Alessandri, R.

Publications and source records attributed to Alessandri, R..

3 recordsLinked to original sources

Detection-Guided Beamforming for Efficient Bat Localisation

Passive acoustic monitoring is widely used to study wildlife, but current approaches provide limited insight into the spatial behaviour of animals. In bat ecology, reconstructing flight trajectories is essential for studying habitat use, movement patterns, and interactions, yet it remains difficult to achieve under field conditions. Acoustic cameras offer a potential solution by enabling sound source localisation, but their practical application is limited by the computational cost of beamforming and by the non-stationary, broadband, and transient nature of echolocation calls. In particular, exhaustive beamforming over wide ultrasonic bandwidths and dense spatial grids becomes infeasible for continuous monitoring. In this work, we propose a detection-guided beamforming framework for efficient localisation of free-flying bats. The method exploits the sparsity of echolocation signals by restricting beamforming to detector-identified time-frequency regions and combines this with physically consistent short-time analysis parameters and dense spatial sampling. The framework is evaluated on field recordings acquired with a Sorama CAM iV64s acoustic camera. Results show that detection-guided processing reduces the number of beamformer evaluations by approximately 77 times, corresponding to a reduction of about 98.7 % in computational effort, while preserving spatial resolution. At the same time, the proposed parameter configuration improves the stability and sharpness of reconstructed trajectories by avoiding artefacts associated with temporal averaging. These findings demonstrate that high-resolution acoustic localisation can be achieved under realistic computational constraints, supporting the integration of acoustic cameras into ecological monitoring workflows. The proposed framework enables the extraction of spatial trajectories from passive acoustic monitoring data, facilitating spatially resolved analyses of bat behaviour in field conditions.

bioinformatics↗

Community Web Portal for Open Collaboration in the Martini Force Field Initiative

AO_SCPLOWBSTRACTC_SCPLOWThe Martini coarse-grained force field is widely used for biomolecular simulations by a large and rapidly expanding community worldwide. Over time, the development of Martini parameters, tools, and documentation has become increasingly dispersed across numerous research groups, leading to fragmentation and making it challenging for users and developers to keep track of the latest models, software, and best practices. Consequently, the development of Martini as a genuinely community-driven process has grown into a bottleneck. In response, the Martini Force Field Initiative (MFFI) has been established as an open-science effort to coordinate and support the collaborative development of all Martini resources. Here, we introduce the MFFI web portal, a platform designed around five core pillars: (i) avoiding reliance on a single group or local server; (ii) minimizing long-term maintenance overhead; (iii) reducing technical barriers for contributions; (iv) providing a unified home for parameters, tools, tutorials, example workflows, and research outputs; and (v) enabling timely dissemination of updates to the community. To achieve this, we use Quarto to generate a static website authored in Markdown, lowering the technical barrier to making contributions, and serverless architectures on Amazon Web Services for scalable, event-triggered backend operations. The source code is hosted in a public GitHub repository under an MIT license, with automated deployment via GitHub Actions and a contribution model based on pull requests for quality control. This design creates a sustainable, low-maintenance, and collaborative infrastructure that consolidates Martini resources and supports transparency. More broadly, our design exemplifies a transferable pattern for building open, community-oriented platforms for molecular modeling and computational science.

biophysics↗

CRANBERRY: An RNA Dynamics Model with Sugar Puckering and Noncanonical Base Pairing

We introduce a new coarse-grained model ''CRANBERRY'' that incorporates sugar puckering and non-canonical base pairing, two factors central to RNA structure and dynamics, yet rarely included in most coarse-grained models. Our model is parameterized through a contrastive divergence approach, combined with fine-tuning strategies to improve accuracy in generating disordered states, a feature that is critical for the accurate description of thermodynamics. This two-stage training procedure greatly enhances cooperative folding behavior. Due to these advances, the model's predictive performance is comparable to that of all-atom force fields for native-state structural fluctuations. Furthermore, CRANBERRY exhibits better agreement with experimental data on stacking free energies and disordered structures measured by Small Angle X-ray Scattering. In addition, CRANBERRY can reversibly fold tetraloops with a minimum RMSD of 1.4 Angstrom de novo, which continues to be challenging for all-atom models. It predicts melting temperatures in agreement with experimental values, and with a greater cooperativity than all-atom predictions.

biophysics↗