802 research outputs found
Femtosecond Coherent Vibrational Dynamics of Anabaena Sensory Rhodopsin
The photo-induced isomerization of retinal protonated Schiff base (RPSB) inside the protein
pocket is one of the fastest (<ps) and most stereo-selective photochemical reactions in nature. The
ground state structure of the RPSB and its surrounding protein constructions are thought to be the
two most crucial factors to drive this reaction. The investigation of each factor individually was
the main goal of this thesis. Anabaena Sensory Rhodopsin (ASR), a recently discovered microbial
retinal protein, serves as an ideal system for this study as it binds two structural isomers (all-trans:
AT and 13-cis: 13C) of the RPSB within the same protein constructions in its photocycle. In the
present work, the photo-induced dynamics of the RPSB in ASR has been explored with the help
of time resolved coherent vibrational spectroscopic methods, which monitor the photo-induced
sub-ps structural changes of the RPSB. These studies have helped to shed light on the intricate
relationship between electronic and vibrational dynamics of the RPSB.
In the first half of this thesis, a comparative study showed both electronic and vibrational dynamics
are widely distinct for the AT and 13C isomers of the RPSB in ASR. In particular, the 13C isomer
exhibited more than five folds faster dynamics than the AT isomer. One possible molecular origin
behind this dynamical difference was found by comparing the ground state Raman spectra of the
two isomers. It depicted an increase in the amplitude of hydrogen-out-of-plane (HOOP) modes for
the 13C isomer, which is usually considered to be an evidence of distortion in the ground state
structure for the retinal system. The ground state pre-distortion has been reported as a potential
element for the acceleration of the isomerization reaction for the 13C isomer, in analogy with the
cis isomers of visual rhodopsin and bacteriorhodopsin.
The second half of this work explored the role of the part of protein helix inside the retinal pocket
as well as that far away from the pocket. In particular, the replacement of the amino acid residues
in vicinity of the RPSB by point mutation caused an acceleration of the reaction rate for the AT
isomer, but it had only a minor effect for the 13C isomer of the RPSB. Furthermore, the truncation
of the part of the protein, embedded into the cytoplasmic region, affected the formation of the
primary photoproduct. All these experimental results lead to two major conclusions of this thesis:
(i) the protein constructions govern the retinal isomerization dynamics and (ii) the same protein
cage exerts differential interactions on two structural isomers of the RPSB
Enhancing Small Object Encoding in Deep Neural Networks: Introducing Fast&Focused-Net with Volume-wise Dot Product Layer
In this paper, we introduce Fast&Focused-Net, a novel deep neural network
architecture tailored for efficiently encoding small objects into fixed-length
feature vectors. Contrary to conventional Convolutional Neural Networks (CNNs),
Fast&Focused-Net employs a series of our newly proposed layer, the Volume-wise
Dot Product (VDP) layer, designed to address several inherent limitations of
CNNs. Specifically, CNNs often exhibit a smaller effective receptive field than
their theoretical counterparts, limiting their vision span. Additionally, the
initial layers in CNNs produce low-dimensional feature vectors, presenting a
bottleneck for subsequent learning. Lastly, the computational overhead of CNNs,
particularly in capturing diverse image regions by parameter sharing, is
significantly high. The VDP layer, at the heart of Fast&Focused-Net, aims to
remedy these issues by efficiently covering the entire image patch information
with reduced computational demand. Experimental results demonstrate the prowess
of Fast&Focused-Net in a variety of applications. For small object
classification tasks, our network outperformed state-of-the-art methods on
datasets such as CIFAR-10, CIFAR-100, STL-10, SVHN-Cropped, and Fashion-MNIST.
In the context of larger image classification, when combined with a transformer
encoder (ViT), Fast&Focused-Net produced competitive results for OpenImages V6,
ImageNet-1K, and Places365 datasets. Moreover, the same combination showcased
unparalleled performance in text recognition tasks across SVT, IC15, SVTP, and
HOST datasets. This paper presents the architecture, the underlying motivation,
and extensive empirical evidence suggesting that Fast&Focused-Net is a
promising direction for efficient and focused deep learning
Signature Verification Approach using Fusion of Hybrid Texture Features
In this paper, a writer-dependent signature verification method is proposed.
Two different types of texture features, namely Wavelet and Local Quantized
Patterns (LQP) features, are employed to extract two kinds of transform and
statistical based information from signature images. For each writer two
separate one-class support vector machines (SVMs) corresponding to each set of
LQP and Wavelet features are trained to obtain two different authenticity
scores for a given signature. Finally, a score level classifier fusion method
is used to integrate the scores obtained from the two one-class SVMs to achieve
the verification score. In the proposed method only genuine signatures are used
to train the one-class SVMs. The proposed signature verification method has
been tested using four different publicly available datasets and the results
demonstrate the generality of the proposed method. The proposed system
outperforms other existing systems in the literature.Comment: Neural Computing and Applicatio
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